I'm fairly sure this is the reason. I seem to remember a few books mentioning (might have been Labyrinth of Evil? Not sure) how as the Clone Wars went on a lot of anti-alien sentiments started to surface, as it was mostly the human loyalists versus the alien separatists, from what the average person could tell. This was likely deliberate on Palpatine's part, and he took advantage of it to help his rise to power. There's no reason to believe he personally hated aliens, at least no more than he hated any one else, he did have a zabrak apprentice after all. Dooku is stated in the RotS novelization to have anti alien sentiments but I don't think that's reflective of Palpatine, especially as Palpatine was already planning to kill Dooku by that point.