Reformation: Who is persecuting who?

I have been reading about the Protestant Reformation, and the general understanding is that the Roman Catholic Church persecuted Protestants who broke away from the church. Most Protestant Reform fell under the leadership of Luther, Zwingli, or Calvin. The only thing is that these same Protestant groups persecuted other protestants. the Anabaptists and Mennonites were groups that did not agree with the Roman Catholic and Protestant Reformers belief that the Church and State should be united. For this, they were mercilessly persecuted in Roman Catholic and Protestant Lands. It is in interesting to me to think that a group that broke away would be persecuted for being to far to the extreme to be in tune with mainstream protestantism. No wonder there are so many different denominations with so many different viewpoints. The Orange County Supertones put out a good question in their 1999 song "One Voice":

And can we sing with one voice, if we all love the same God, can we agree to disagree?

I think we can in spite of all the historical baggage. In spite of all the differences, God can work to build his church through all the different denominations. Different parts, one body.