Stipulating that Christ is referring to Peter, is He referring to Peter as the founder of the Church, or is He referring to Peter's confession, or is He referring to Peter as the prototype believer? We believe the latter two, and our position sophistry in the light of other Scripture. Jesus is the Founder of the church. His words that if men did not praise him, the rocks and stones would cry out show that His purposes would be achieved without the cooperation of men, though it was His pleasure it did.
Protestantism did not alter the Church; Protestantism restored the Church to positions closer to the Church Fathers, by relying solely on Scripture, solely on the grace of God, solely on faith as the instrument of grace, and solely on salvation being God's work alone. You may disagree with this. It's pretty clear that salvation is of the Lord alone; and He has allowed formulaic disunity of churches to provide a place for all His Body.