This is one dude even Horus doesn't want to mess with. When he appears in the Rio Grande, Carter is like, uh oh: "[T]he guy was twenty feet tall… His chest and arms were human, but he had light green skin, and his waist was wrapped in a green armored kilt like reptile hide. He had the head of a crocodile, a massive mouth filled with white crooked teeth, and eyes that glistened with green mucus… His black hair hung in plaits down to his shoulders, and bulls horns curved from his head" (30.100). Nasty.
According to Horus, who's giving Carter the DL in his head, Sobek only understands strength. This is why he used to be a supporter of Ra, the sun god, and of Osiris, the king (when he was alive). He's siding with Set this time around, though, because Osiris is dead (again), and Horus's current host is too weak.
Unfortunately, Sobek is right: even when Carter summons his warrior avatar, he's too weak to defeat Sobek, and Bast has to sacrifice herself to do it. Why is Sobek so hard to defeat? He tells us, conveniently enough: "I am lord of the water! My sweat creates the rivers of the world!" (30.124). First: gross. Second: we can see why he's a powerful dude. Too bad he's not on the side of the good guys… but it goes to show how easily power corrupts.