Because the Doctor looks like a human, sounds like a human, and always hangs around with humans, we often forget that the character is just as much of an alien as the Slitheen, the Judoon, or even the Daleks are. Minus the gooey squid monster.
This is a character from another planet, a character who was raised in a radically different culture, a character who has lived for a mind-boggling amount of years. And so, even though the Doctor likes to mingle with us lowly humans, there are many, many occasions where the character's "alien-ness" fully shines through: eating fish custard without puking, performing acts of scientific genius, and also, treating his companions like they're nothing but dirt beneath his fingernails.
Whether he's intendingto be a dick or whether he does it by accident, there are times when the Doctor doesn't seem all that bothered about his companions during the modern series, which can damage them emotionally, turn them against him, and sometimes, even put their lives in danger.
The Doctor's people skills definitely need some polishing, and because his companions are around him all the time, they know this better than most.