Before I dive into your questions, I think we can all agree that allowing Muslim immigration was and is a mistake. Once these people are in your country, they are in your country. If you want to get them out, the only way to do so is through deportation. Deportation is the wisest answer, but it's not on the table for any Western European country at the moment so we can assume the millions of migrants are here to stay for awhile.
As a general rule, seeing people clearly for who they are is preferable to not. And since they're here to stay for the foreseeable future, knowing what you are up against is preferable to not. For example, if some bullies are planning to kick my ass after school, I'd much rather prefer they announce their intentions instead of keeping it a secret. With the former, I at least have a chance to evade them. With the latter, I'm just going to be jumped and pummeled while I walk home.
By suppressing the flag you do not make the problem go away, you're only making it go underground where it's less visible to non-Muslims and in this sense more dangerous.
Your question: "Aren't their true colors patent?" Well, no, they're not. They are to you. They are to me. But they're not to everybody, or else we would be addressing the problem.
And to your last question: They are already out in the streets marching. Imagine if instead of Turkey's flag those were ISIS flags. Wouldn't that send a stronger signal to Europeans about the danger they're in?