There are a few different reasons why Persians are considered the bad guys and the Greeks the good guys. The main one is cultural perspectives. Right now, the United States have less than friendly feelings towards Iranians. As such, it would be unwise (from marketing point of view) to portray Persians as anything but bad guys. The people there are subject to all manner of evil tortures and punishments for even the slightest thing, including such as criticism of the government. The second reason is political propaganda. Persia (Iran) remains backward in the eyes of the Western World and today still has no democracy. When Hollywood portrays Iranians as evil, mutated savage monsters, the image subconsciously settles in people's minds. Decades ago, the standard villain was Russian with horrible aspect, which reflected the Cold War and its aftermath. Right now, Iran is (or is made to be) the enemy, so they are not going to get any good press.
The third reason is historical accuracy. During the Greco-Persian Wars, the Persians were the bad guys, if only they were the attacking side. The Greeks didn't try to invade Persia (at least, until Alexander of Macedonia), it was the Persians who attacked first.
Because Greek culture has had a much more profound effect on European (and by default, American) culture and history, our sympathies are always going to be on their