It started with the Roman Empire.
Official policy was simple - you could have any and as many religions as you want, but there was only one government: Rome. Problem was, there were two religions that were the government: Judaism and Druidism. The Druids decided it wasn't a bad policy and politely faded away. The Jews fought tooth and nail - millions died and are still dying.
Christianity and Islam, as descendents of Judiasm, have always wanted to be the government, and the Church of Rome pretty much pulled that off. For a long time the only real resistance was the Masons, rooted in Germany where the power of the Church was a bit iffy.
The foundation of the U.S. was a Masonic plot, which is why our government is so different from what went before, and why the "Great Seal" of the U.S. is entirely Masonic symbolism. Naturally, the Masons were wary of the churches.
The Christians fairly quickly moved into the government, and tried to get rid of the Great Seal and other Masonic trapings, but have been held in check by the law. This has been a continuing church/state battle.
As for Pagan symbolism, while there are Pagans today, and some few favor the Classic pattern of abstraction (most chose Egyptian, Celtic or Eastern patterns), they are no threat whatever because they do not seek in any way to be the government - what they want from the government is protection from the Christians, who would very happily murder every non-Christian in the world if not held in check by the law - and who are a direct threat to government because they want to be the government.
Christian icons on government property are a direct threat not only to non-Christians but to the government itself and cannot be tolerated. Pagan symbolism is just that, abstract symbolism - neither an object of worship nor a threat to government or to people of other religions.
