The A.C.L.U. - A Contradiction

The American Civil Liberties Union or A.C.L.U. is suppose to be an organization who sole purpose is to protect and preserve the rights of all citizens of the United States as found in the Constitution. So why is it that they work so hard to trample on the very rights they strive to preserve while attempting to protect the same?
I give you school prayer. Now, as a Christian I do not condone teacher led prayer in schools. I do not want a person who may not be a Bible believing Christian leading my children in prayer, but let us use this example to see a clear contradiction that is the A.C.L.U. This organization claimed that to have prayer in school infringes on the rights of those who do not want to pray or practice religion. But what about the rights of those who do? I believe that they are stomping on the First Amendment rights of those who have a desire to have free speech and expression of religion.
How about Affirmative Action and other such regulations? In making sure you have just the right number of minorities employed at a workplace or enrolled at a college or university, are we not infringing on the rights of the Caucasian? I do not care what color you skin might be, I want the right person for the job. I want the he or she that has the best training, experience and/or personality to fill the niche.
A.C.L.U. if you have to exist, please exist for all people and not just those who make more of a statement and get you more press, not just the left, but the right.