The problem is something that can't be understood as easily as you all may think, just because too many people think that religious freedom = allow EVERYTHING.
Just think of this: why the major problems are related to Islamism? Why does it seem more problematic than other religions?
The truth is that Muslims are difficult people to deal with. I don't pretend to judge every Muslim, but they generally tend to practice (in a more or less aggressive way) their own customs and habits beyond their personal space. They go to live to other countries but they pretend to live the same way they live in their origin country, they don't care if the new country has a different culture or religion.
There are so many examples... Don't you remember what happened in France some years ago when a lot of Muslim youngsters revolted against the police and burnt cars? Even in this case, the criticism towards them wasn't allowed and "it turned out" that they were some kind of heroes revolting against the discrimination towards Islam... ¬_¬
There are more cases in France or in Spain (as far as I know) where Islamics don't respect the rules about noise levels (their early prayers, for instance or... surprise! the use of minarets for their call to prayers) and healthiness at their houses or worship places. But don't worry if you're a Muslim, when the local authorities ask you to accomplish the law that EVERYBODY must obey, you can just throw the "xenophobic card" and go to the media.
I know a case of a Muslim that didn't want to pay his part of neighbourhood expenses because the president of the Community Committee was a woman, at that time. In some other towns, they asked the local authorities to close the swimming pools to the general public, one day a week, for their women to take a bath. Some Muslims openly say that they want to spread the Muslim kingdom "with the wombs" of their women (this happens in Spain, especially, where they had been reigning after an invasion, back in the 8th century).
On the other hand, as a Christian you can't go to a Muslim country and openly profess your faith, in most of the cases.
Some European countries are worried about this issue, but they are not even allowed to show their concern because they would be automatically catalogued as racist and intolerant.
Yes, Muslims MUST have their freedom, but so does the other people.