First, when Jesus said "Upon this rock I will build my church," he was referring to Peter. I say that because the two Greek words - petros and petra - basically mean the same thing. They are different forms of the same word. One is masculine and the other is feminine. That's the only real difference. Jesus was saying, "Peter, you are a rock-man."
Second, when Jesus said, "Upon this rock I will build my church," he said it after Peter made his great confession of faith. The timing is crucial. It's not as if Jesus looks around and says, "Well, you're the best I've got so you'll have be the one." No, Jesus wasn't looking for some fall guy on which to build his church. Peter could not have been the rock until he made the great confession. That is, the rock is not Peter the doubter or Peter the denier. The rock is Peter the believer and Peter the confesser. The rock is Peter as he publicly confesses that Jesus is the Christ, the Son of the living God. Upon that rock Jesus will build his church.
Third, when Jesus said, "Upon this rock I will build my church," he said it to Peter as representing all the apostles. Remember I mentioned that the question was in the plural - "Who do you (plural) say that I am?" Jesus wasn't asking Peter alone; he was asking all of them. When Peter answered, he wasn't answering only for himself; he was answering for all of them. And when Jesus said, "You are the rock," he wasn't speaking of Peter alone. He was speaking of all the apostles.
I think Jesus was saying, "Peter, you are a rock. And upon you, and men like you, I will build my church." Now, to say that is not to agree with everything else that other people may say about Peter being the rock. But it is to say that Peter is the foundation of the church in the sense that, when he made that confession - and all the apostles with him - he was the rock - and they were the rocks upon which the church is built.
Excerpted from "Upon This Rock" by Keep Believing Ministries (used by permission).