Although I don't grant the assumption that aliens are portrayed as hostile by default, they are certainly portrayed that way in a substantial percentage of pop culture instances, so I think the basic question of "why? [http://www.youtube.com/watch?v=wMFPe-DwULM]" is still valid.
At a superficial level, the point that dumb action movies make lots of hay with hostile, morally unambiguous antagonists who can be slaughtered wholesale cannot be ignored. Nazi, terrorists, mercenaries, and insect-like aliens- what would we do without them?
On a deeper level, I think the enduring human characteristics contribute to this. I'm talking about xenophobia and inferiority/superiority complexes. Sometimes these were products of their times, such as the monster movies of the 50s and even Well's War of the Worlds. The Man Who Fell To Earth dealt with this in a meta fashion.
You can also look at it from a historical perspective. I recognize the futility of applying human behaviors and motivations to creatures who probably have less in common with us than we do with a termite mound, but there might be some value in looking at the model for contact between human cultures who are not on very similar levels of development. It usually ends badly for the "primitive" ones. See: Gauls & Romans, Celts & Romans, Indians & Europeans, Africans & Europeans, Native Americans & Europeans, Chinese & Europeans, Mainland Asians & Japanese, and Local Businesses & Wal-Mart. Conflict seems to be inevitable unless the more advanced society is going through a guilt-ridden phase.
Really, though- there's no story without conflict. And conflict with aliens is easy to write.