I think you are right. It is not that the ACLU is pro-Muslim. It is that it is something different than mainstream and thus something to be tolerated and protected.
Activists seem to get off on protecting the different.
According to the by-laws of the aclu, their first and foremost objective is to overthrow the government of these United States and replace it with a communist government. That’s it’s only objective, no matter how they cattawhal otherwise, that is the reason the aclu was put together by a bunch of communists lawyers.