As a preamble, I don't want to attack your faith.

However, the argument here is not that Christians side with the elite, but that the Church does. The Church has sided with the powerful again and again over the centuries, to great effect for its own wealth, going against what was objectively (ie not only by today's standards) morally right, and very much against scripture.

Your own argument that submission to God supersedes submission to government is one that the Church, as an institution, rarely abides by. By any reasonable reading of his sayings, Jesus would have preached against oppression of the poor, slavery, war, politically-convenient massacres, even the selling of indulgences. From the 4th century on, the Church has been part and parcel of oppression in all its forms, at enormous benefit to itself, and often against what the oppressed wished.

The changes that the Church made to early Christianity (centralisation, violent standardisation of beliefs, empowerment of the clergy) might have been sincere, but the continuing plight of the poor while the Church became one of the richest and most powerful institution in this part of the world is difficult to see as an an unfortunate coincidence.

If the Church is happy to call for the killing of peasants while at the same time initiating and celebrating massacres during the Crusades (a period of a Christian caliphate), among many many examples, it's only right that the institution be seen as an oppressor that has not much in common with Jesus or Christians.

Again, I'm not talking about Christians, or even individual priests, but the institution itself. I think Jesus had beautiful ideas, but it's difficult to know anything about history and not despise the Church.