The Catholic Church has a history of wars and abuse of power by its leaders, and it even had three popes at one time. Given that, how can we believe Christ founded the Catholic Church?
Let’s re-phrase the question using a modern analogy: The United States of America has a history of wars and abuse of power by its leaders, and it even had two presidents at one time. Given that, how can we believe that the Founding Fathers created the United States?
By substituting a modern political reality, it is easier to see the faulty premises upon which the argument against the Catholic Church was built. Just as the United States did not ever have two presidents at one time, only a period in late 2000 when there was a question over who was the rightful president of the United States, so the Catholic Church never had three popes, only a period when there was question over who was the rightful pope. And, in the same way that the checkered history of the United States does not invalidate the historical reality of its creation by its Founding Fathers, so the dark periods of Catholic history do not invalidate the historical reality that the Catholic Church was founded by Jesus Christ, who himself expected that humans would fail miserably (cf. Matt. 13:24-30) but promised to protect the Church and preserve it to the end of time (Matt. 28:19-20).