A religion is an ideology, and as such is a competitor with other ideologies such as nationalism. The Syrian government feels free to do a lot of things. But it isn't free to simply tear down all the mosques and announce that assemblies on Friday are illegal and will be punished.
In the Syrian case the situation is complicated by the fact that the government is dominated by an arguably heretical Muslim sect, which limits its ability to co-opt the major Islamic groups within the country-contrast that to the situation in Iran, where the government is controlled by the majority Twelver Shia sect. During the Nazi period, the Christian churches did not, so far as I can judge, do an awful lot to constrain what the governments were doing, although of course some individual Christians did. But still competition, even limited competition, is valuable. Even in Iran, I suspect the government is to some degree constrained by the fact that prominent Shia scholars have reputations and from them authority that doesn't derive directly from any official position.