When the sight of a few people waving rainbow flags at a pop concert becomes an act of "moral terrorism", when it plunges a country into hysteria and the government responds by arresting dozens of people on suspicion of being gay and orders the media to show them no sympathy, it's time to ask why.

Such was the apparent power of these flags that Egypt has been in paroxysms over them for the last couple of weeks. But to treat this as a case of mass homophobia, or even hyper-homophobia, misses its real significance. At the root of the rainbow flags affair are two fundamentally opposing views of where Egypt is – or should be – heading.

This clash over Egypt's future has many aspects, and liberty of the individual – sexual behaviour included – is one of them. On one side are those, like the head of Egypt's Supreme Council for Media Regulation, who say homosexuality is disgraceful and the media must help stamp it out. On the other are those who say what happens between consenting adults in private is no concern of the state, the police or anyone else.

Egypt's war on rainbow flags: a compilation of blog posts

The dispute here is not so much about sex itself as about the role of the state and society in policing it. Why would a government – and a regime like that of Abdel Fattah el-Sisi in particular – bother with such matters? And why, having decided this is proper government business, would it side with those who are fearful of what others might be doing in darkened rooms?

The short answer, of course, is that it's playing a populist card. There's far more political mileage to be had in Egypt from attacking LGBT people than defending them. Minorities – especially small and unorganised ones – are an easy target and if they can be portrayed as a threat to the nation's well-being, so much the better. We have seen this in Egypt before, with atheists and Shia Muslims, and especially with the notorious "Queen Boat" case of 2001 which involved 52 allegedly gay men. 

The Queen Boat defendants were tried in  the state security court, specially set up under an emergency law to deal with suspected terrorists. A Cairo newspaper reinforced this "security" angle with a front-page headline that said: "Perverts declare war on Egypt".

The message that homosexuality is unpatriotic was hammered home by al-Musawwar magazine with a doctored photograph of Sherif Farhat, the main defendant in the case, wearing an Israeli army helmet and sitting at a desk with an Israeli flag. Meanwhile, the semi-official al-Ahram al-Arabi magazine headlined a spread of articles with the words: "Be a pervert and Uncle Sam will approve".

In the current furore there are repeated attempts to link "promotion" of homosexuality (for example, by waving a rainbow flag) as a form of terrorism. In this fantasy world it was only a matter of time before the customary but unspecified "foreign hands" would make an appearance – and, sure enough, they have. 

According to Youm7 newspaper, the concert flag-waving was not just flag-waving but the signal to launch a foreign plot:

“Security investigations found that some of the accused in the case received funds from foreign bodies and rights organisations calling for freedoms to execute a plan to spread thoughts calling for the breakdown of society and spreading ideas that undermine public conduct and morals. Raising the flag at the concert was a signal to these organisations that the plan is being implemented.”

What Egyptians are meant to conclude from this is that the only thing protecting them from the foreign-gay-terrorist onslaught is the Sisi regime. Posing as guardian of the nation's cultural, religious and moral values is a familiar tactic among Arab regimes. It provides a veneer of respectability and gives them a measure of legitimacy which would otherwise have to be acquired through the ballot box. As a general rule of thumb, this preoccupation with national values and morality tends to be inversely proportional to the regime's actual morality in terms of brutality, levels of corruption, and so on.

In Egypt's case there are a few additional factors. One is the regime's long-running war against the Muslim Brotherhood: while cracking down on Islamists it needs to display religious credentials of its own. Turning the rainbow flags affair into a public spectacle also creates a welcome diversion from the country's real problems.

Sisi heads an authoritarian regime ruling over what is still, for the most part, an authoritarian society, and the regime's attitude to rainbow flags and LGBT rights is probably not very different from the attitude of most Egyptians. In that respect, no one can seriously claim the regime is out of step with society.

It is not abnormal for the attitudes of government and society to reflect each other and, if left to their own devices, to evolve more or less together over time. Problems start when this evolution is not allowed to take place – as we are now seeing in Egypt.

The "traditional" values espoused in most of the Middle East are less traditional than many suppose and are, to some extent, imaginary: look at the way Egyptian women are dressed in photos and films from the 1950s. The dangerous part, though, is that they are presented as fixed, unchanging and unchangeable.

This is what the Sisi regime is doing in connection with LGBT rights. Instead of allowing rational discussion – and the possibility of a shift in public opinion – it is insisting that nothing can change. It has given instructions that gay people must not appear in newspapers, on radio or television unless they are appearing to publicly repent. It has given orders that the media must portray homosexuality as a disease which, with proper treatment, can be eliminated.

This may prove a trickier approach to maintain than the regime imagines – not least because it doesn't explain why the "diseased" are being collected by police cars rather than ambulances. To many outside the country, if not inside, this approach also makes the regime look ignorant.

Further evidence of the regime's ignorance comes from its ordering of anal examinations on suspects "to determine if they have committed homosexual acts". Such tests are not scientifically valid and are widely regarded as medically unethical. There was also that embarrassing episode a few years back when the Egyptian army developed a "miraculous" magnetic wand which it claimed would cure HIV, hepatitis C and other viruses.

Although there are many similarities between the rainbow flags affair and the 2001 Queen Boat case, it may not turn into a simple re-run this time. In 2001 there were virtually no voices in Egypt supporting the Queen Boat defendants – even the main local human rights group shied away – but there were no social media then and the internet has since given many Egyptians new perspectives, especially among sections of the urban youth. Some even think it's cool to have gay friends.

Since 2001, Egypt has seen both revolution and counter-revolution. In the counter-revolutionary phase many have become so dispirited as to abandon any thoughts of continued struggle. Regardless of that, though, resistance over the rainbow flags affair looks like being stronger than it was over the Queen Boat.

One pointer came in 2014 when a TV reporter accompanied police on the raid of a Cairo bath-house which the reporter described as "a den of perversion". Instead of the customary applause for this exploit, however, the reporter faced a barrage of social media criticism.

Unlike the Queen Boat case, some of the rainbow defendants appear defiant and have aleady been speaking out, if only through their lawyers.

Sarah Hegazy, the only woman among the dozens arrested, claims she was beaten in her cell by fellow inmates after police them she was involved in a case relating to homosexuality.

Another defendant, Ahmed Alaa, not only admits waving a rainbow flag but defends his right to do so. Mada Masr reports:

Alaa was questioned for hours simultaneously by another prosecutor, according to his lawyer Ramadan Mohamed. When asked about his sexuality, Alaa responded that he isn’t gay. “I am not a member of the homosexual community, but my personal belief is that every person is free, as long as they don’t harm others, and I don’t know anyone from this community personally,” he said, according to the lawyer. 

When asked about the raising of the flag at the concert, Alaa explained that it happened sporadically and wasn’t planned. He said he didn’t bring the flag to the gig, but borrowed it from another member of the audience.

The prosecutor told Alaa there is a contradiction between his “accepting of homosexuals,” and his knowledge of the Quran, in which “homosexuality is condemned,” to which he responded, “The state permits the selling of alcohol, despite it being prohibited by Islam. Every person is free, as long as they don’t harm others. They will be judged before God in the end. The law does not punish personal beliefs or sexual practices.”

A video in support of Alaa, which was posted on YouTube yesterday, has so far had more than 88,000 views.

The rainbow flag defendants certainly have support, though how strong it will be remains to be seen. Once again, the regime may succeed in swallowing its victims whole. But this time it could find them surprisingly indigestible.