Consider Antonio's behavior and dialogue in Act 1, Scenes 1 and 3 of "The Merchant of Venice". Why does he treat Shylock the way he does? Is it justified?

Antonio does not mention much about Jews or Shylock in scene 1, so one cannot ascertain his opinion here. However, his prejudice against Shylock is pertinently obvious in scene 3. He clearly does not like Shylock mostly, it appears, for the fact that he deems him materialistic and greedy for money. When Shylock refers to Biblical scripture to justify the fact that he charges interest on money which he lends out, Antonio is quick to criticize and admonish him for daring to use scripture in this context. When Shylock relates the biblical story of Jacob profiting by taking possession of the offspring from Laban's sheep, Antonio tells him:

This was a venture, sir, that Jacob served for;A thing not in his power to bring to pass,But sway'd and fashion'd by the hand of heaven.Was this inserted to make interest good?Or is your gold and silver ewes and rams?

The implication is, therefore, clear. Antonio believes that one should not deliberately seek to profit from others. It is, however, acceptable if such a boon is provided through an act of nature (i.e. divine intervention). Shylock, on the other hand, seeks to deliberately profit by charging interest. Greater criticism lies in the fact that he deems Shylock to be deceitful, misleading and manipulative for he states:

Mark you this, Bassanio,The devil can cite Scripture for his purpose.An evil soul producing holy witnessIs like a villain with a smiling cheek,A goodly apple rotten at the heart:O, what a goodly outside falsehood hath!

Further evidence of Antonio's antagonism lies in the fact that he does not apologize for the despicable manner in which he had treated Shylock on a variety of occasions. When the Jew tells him about his derisive treatment, Antonio declares:

I am as like to call thee so again,To spit on thee again, to spurn thee too. 

The question of whether Antonio's hostility is justified depends entirely on the context of one's approach. Christians and Jews have shared a hostility throughout history - since Christians believed that Jesus had been betrayed by the Jews when they refused to accept him as the Messiah and denounced him. Christ was crucified as a consequence. Furthermore, Christ was severely critical of usury and warned against its use during his lifetime. Christians, as followers, obviously adopted his teachings.
In this context then, one could argue that Antonio's disapproval is justified. From a Christian perspective which teaches that one should 'love thy neighbor as thyself,' though, it is difficult to understand Antonio's loathing. Furthermore, the fact that Antonio is prepared to, as he states, 'break a custom' smacks of hypocrisy. 

Shylock, although I neither lend nor borrowBy taking nor by giving of excess,Yet, to supply the ripe wants of my friend,I'll break a custom. Is he yet possess'dHow much ye would?

In the final analysis, one has to conclude that the characterizations are the result of a brilliant author's rich imagination and serve a particular purpose - to create a story and create drama to enthrall and entertain a captive audience.