why do elves and dwarves not really get along? e.g. legolas and gimli (in the beginning anyway)

It's partly because of their nature and partly because of the fact that elves used to blame dwarves for awakening Balrog in Moria. The conflict in the First Age between the elven king Thingol and dwarves caused by Silmaril and resulting in dwarves invading Doriath and killing Thingol is probably another reason.

The only way to answer your question is asking you : Why do cats and dogs don't get along?... They're natural enemies, just like vampires and werewolves, vegetarians and meat, hippies and hunters, etc =D

I think it's in their nature....like gomukiller said