Absolutely. As such, any legislative or judicial action that favors atheist causes/groups/plaintiffs/etc. amounts to ACTUAL government endorsement of one religion over another.
What has actually happened is that the state has imposed a religious belief throughout all government institutions, including schools. When it, for instance removes the Ten Commandments from a school or forbids the mention of God, it is interjecting another religious belief in its place, Atheism. Just as every religion adheres to a set of moral principles, so does Atheism. The entire homosexual agenda is a manifestation of an atheistic dogma. The attacks upon the divinely instituted definition of marriage, the worship of the environment, the denial of absolutes, the denial of truth, and denial of a soul are all doctrines of Atheism.