I've known and worked closely with several lawyers who were members of the ACLU. Everyone of them fairly religious, honest up standing men...and one women. The ACLU gets a bad wrap because they defend anyone whose rights have been denied. As a result they've ended up taking sides with some pretty unpopular causes. Law enforcement has been known to bend the rules. It happens, I've seen it happen. When short cuts are taken, peoples rights get violated. IE illegal searches, wire taps etc... The ACLU will often take on cases where the government has done some illegal action and violated the rights of some person or some group. One famous case involved a wire tap and a group known as NAMBLA or the North American Man Boy Love Assoc. A group of pedophiles who like to sleep with under age boy. Jon Stewart of the Daily Show like to refer to any group he doesn't like as "NAMBLA." Anyway the feds tapped this groups phone without the proper warrants and gained info used to arrest several members. The ACLU stepped in and the case was thrown out. So people don't see it as protecting Constitutional rights, but rather as support for groups such as NAMBLA, Nazi's et el.
They've also stepped in and supported people who have felt their rights were being infringed on by churches. Such as displaying the Ten Com. or not allowing their children to join groups like the Boy Scouts due to their child's lack of religion. So people have labeled them as being anti-church. They're not anti-church- they're pro US Constitution. In fact on many occasions they've stepped in and supported the church and religious people too when their rights were being violated. They've come to the defense of students who wanted to pray in school and were being told they couldn't. Here's a link on one such case:
http://www.laaclu.org/News/2003/April%2016%20School%20Prayer%20HB.htm
Bottom line is the ACLU will step in and help anyone who's Constitutional rights are being violated. Rush Limbaugh has spent years bad mouthing the ACLU. He's called them everything form evil to un-American. When Florida prosecutors wanted his medical records pertaining to his drug abuse who'd he call? The ACLU...and they took his case. They're not anti-American or anti-church. They are pro US Constitution.