Easy answer: The ACLU is not interested in the so-called separation of church and state. They are anti-Christian, anti-Catholic.
They will fight for the right of muslims, buddhists, satanists, etc., to pray or worship in school, colleges, universities, but Christians? NO WAY!
If they went after every religion equally, they might (and I emphasize MIGHT) have a little more credibility.
The ACLU is anti-American, anti-White, anti-Christian, anti-business, anti-state's rights, anti-military, anti-law enforcement. They are pro terrorist, pro marxist, pro deviants, pro illegal drugs, pro anarchy.
Unfortunately I believe it will take quite a few more years before the general public rises up against them.
The first thing that should be done is to cut off their public funds!
don't worry they are working up to anti-Jewish. That is to overt to spout just yet. But there will be an issue they can jump onto sometime.
The ACLU is like the Shadows (sf ref to Babylon5)