It was a simple issue, one that could have been worked out easily had the two men decided to just get along. Shylock could have made any number of better choices in this situation: forgive Antonio, since he lost his ships; pocket Portia's offering of double the amount Antonio owed him; worked out a new time frame in which Antonio could have paid him; and so on. What he did was exactly the worst possible choice (we know this because he ends up losing pretty much everything and is forced to convert to another faith). He was so intent on getting his revenge on Antonio (and possibly all Christians indirectly) that he was completely blinded to reason.
So, what led to Shylock's loss of good judgment? He blames it all on the way the Christians treat him and his people; I am inclined to agree with him, up to a certain point. At the time the play was written, Christians were often intolerant of all people of other faiths, not just Jews. Because of this, we can see that this is not just a problem with a specific group of people; it is an issue of Christians versus everyone else, an intolerance of anyone who is different.
This intolerance makes Christians appear hypocritical in The Merchant of Venice. Shylock's argument in his monologue in Act III is that both Christians and Jews are both simply human beings. They are hurt with the same things, are made the same way, die the same ways, bleed, laugh, etc. They are all people, and Shylock does not understand why they are not treated equally. The Christians hold a double standard: if a Jew wrongs a Christian, revenge is just--however, if a Christian wrongs a Jew, the Jew would be considered a vile and evil person if he or she decided to take revenge. Shylock claims that he is merely following the Christian example by insisting on taking the pound of flesh from Antonio. (He lays waste to the pretensions of the Christian characters to value mercy, charity, and love above self-interest.)
Shylock is the victim of a self-fulfilling prophecy. He says to Antonio, "Thou calledst me dog before thou hadst a cause. / But since I am a dog, beware my fangs." Antonio judged him before he even knew him purely based on the fact that he was a Jew, or an infidel. Thus, Shylock decides that he will act the way he is perceived, since the Christians probably won't change their preconceived notions anyway.
These are just a few examples of Christian themes I've found in the text. It kind of makes the Christians look bad, but then again, they weren't members of the true church... They'll see the light eventually!