I am a BIG fan of Harry POtter audio-books from the local library, and at the monent i am listening to Book One.
I was listening lastnight to when Harry has had his 1st potions lesson, and cam uo with the theory;

Snape knows that by defeating Lord Voldemort, Harry had possesed some of the Dark Lord's power(s).

He may have realised that because of this, Harry MAY be able to come into Slytherin.

This ties in with whether Snape is a goodie or a baddie, beacuse if he is a baddie, he would have wanted to have Harry in Slytherin so Voldemort could get him easier (coz it was inevitable that WOULD come back, i think)

Long story cut short, Snape hates Harry because he CHOSE to go into Gryffindor, and not Slytherin.