[DevinFuture]

Well, I can't speak for them all, but this lefty thinks that neither putting the Quran in the toilet, nor burning an American flag, nor putting a crucifix in a glass of urine is a proper basis for arresting anybody. I don't know why the ACLU wouldn't be interested in taking such a case though. They've had no problem taking cases with a broad range of clients spanning from right wing Nazis to left wing communists.

Hate crimes is an interesting first amendment issue though.
Almost all liberals and conservatives would agree that there are proper limits to protection of freedom of speech. And the Supreme Court has clearly stated that not all speech is protected.
With regard to the Quran in the university toilet, courts have demonstated some willingness to uphold restrictions on "lewd, profane, or indecent" speech where the speech bombards a "captive audience." Perhaps users of a semi-public toilet could be classified as a captive audience. The problem is that courts have never said what consitutes lewd, profane, or indecent speech. So there is no easily applicable test. Lower level judges will continue to draw the boundaries as they see fit unless they are given a more precise test to follow.