It doesn't make sense to me. After the rebellion by Poseidon, Hera, Athena and Apollo, Poseidon and Apollo were sent to Troy as mortals to build a wall. When they finished, Troy's king refused to honor them. This caused angst between them. Then, Cassandra refused to honor her agreement with Apollo (I give you gift of prophecy and you give me virginity/sex).
This is two reasons why Apollo would side against the Trojans, so why didn't he? Does it have anything to do with Iapyx (a favorite of Apollo) being with the Trojans?