Do any Protestant groups teach that Paul founded the Church and not Peter? I have always been told that Peter was the head of the entire Church at the time of Christ.  However, James was apparently leader of the Church in Jerusalem, and Paul started a number of churches outside the Holy Land. Who is considered to be the first leader of the Church established by Jesus according to the various Protestant denominations?
Protestants do not recognize the necessity of a single worldwide leader other than Christ. So it is not as if Peter is dethroned so that Paul can take his place. Both are recognized as important leaders, but not one over the other.

An example of this thinking can be found from John Calvin in the Institutes. In Book 4, Chapter 6, he writes:


  And yet, in truth, none can solve this question better than
     Scripture, if we compare all the passages in which it shows what office
     and power Peter held among the apostles, how he acted among them, how
     he was received by them (Acts 15:7). Run over all these passages, and
     the utmost you will find is, that Peter was one of twelve, their equal
     and colleague, not their master. He indeed brings the matter before the
     council when anything is to be done, and advises as to what is
     necessary, but he, at the same time, listens to the others, not only
     conceding to them an opportunity of expressing their sentiments, but
     allowing them to decide; and when they have decided, he follows and
     obeys. [...] 


After a number of scriptural examples, Calvin concludes:


  All these things make it manifest, either that
     there was an equality between Paul and Peter, or, at least, that Peter
     had no more authority over the rest than they had over him. This point,
     as I have said, Paul handles professedly, in order that no one might
     give a preference over him, in respect of apostleship, to Peter or
     John, who were colleagues, not masters.