Okay, first, there's nothing to suggest Shinigami in general do not like humans. A lot of Shinigami we've seen, officers even, have displayed no animosity or even bigotry towards them. While there are Shinigami that might be bigoted towards humans, that's probably for the same reasons anybody in real life is bigoted towards any ethnic group. As for the protecting, that's their duty. It's the primary duty of the Gotei 13 to preserve the balance. Letting humans suffer mass extermination at the hands of anyone upsets the balance, and is also very immoral and irresponsible.