Legolas eye colour is brown in the three Lord of the Rings movies and I believe Orlando Blooms eyes are brown.
So why does he have blue eyes in the Hobbit?
For the same reason that his eyes are blue in every other film:
Peter Jackson cast Legolas as a blue-eyed elf.
For evidence, look at these countless screen captures showing Legolas.
Note that his apparent eye color varies depending on his surrounding, as is often the case for people with blue or hazel eyes, perhaps leading to the impression that his eyes may have been brown.