I'm not certain, but didn't the whole Persian/Greeks thing start when Athens came to the aid of the Ionians, sacking Sardis, after their revolt was crushed by the Persians?

I'm sure other factors didn't help either:

-The elimination of Lydia as a buffer state.
-Darius' being constantly reminded by Hippias, the ousted Athenian tyrant, that the Athenians wronged him.

But yeah, I don't think there was any ideological hatred of Greeks on the part of the Persians. Just a little mud in the eye.