Tom Riddle is a half-blood, although he's made sure no one knows it. Tom Riddle is the smartest wizard Hogwarts has ever seen (except for maybe Dumbledore, but he doesn't consider Dumbledore actually SMART in any sense of the word). Tom Riddle hates mudbloods, muggles, and all blood traitors. They are vile creatures and their magical talents are mediocre at best.
Hermione Granger is muggleborn, a mudblood. Vile and disgusting and everything he hates. Hermione Granger is quite possibly the smartest witch he has ever met. Hermione Granger is easily the smartest Gryffindor he's ever met.
Tom Riddle thinks he may fancy Hermione Granger. This is not good. Not good at all.