It seems OP's opening assumption that media tends to depict aliens as hostile is .
By way of a little experiment, I looked at this [http://uk.imdb.com/search/title?genres=sci_fi&sort=boxoffice_gross_us,desc] list of top-US-grossing sci-fi films. I paged through the first 100 and listed all of which had aliens and weren't outright kid features. I counted franchises as a single entry on the list, so Star Wars and Star Trek appear once each since each film within the franchise talks about the same fictional universe.
I came up with 16 films depicting aliens in contact with humans. (Avatar, Star Wars, Transformers, Avengers, Independence Day, Star Trek, Men In Black, War of the Worlds (2005), Signs, Super 8, Prometheus, Green Lantern, District 9, Contact, Cowboys & Aliens, X-Files (1998))
Of those, six (Independence Day, War of the Worlds, Signs, Prometheus [debatable], Signs, Cowboys & Aliens, and X-Files [also debatable]) depict aliens which are universally hostile. The other ten either feature friendly/indifferent aliens, or a mix of friendly and unfriendly aliens. Six of sixteen isn't a majority, just a large minority- so by the yardstick of high-grossing US sci-fi movies, the "problem" isn't that severe.
I acknowledge up front that this is a complex matter, and so vulgar a measure as "it made lots of money in the US" is pretty chauvinistic. The approach has problems but I think it's good for a ballpark figure of what's in the Western consciousness.
If we widen the focus to include popular video games, things are probably going to change drastically. I can't think of many popular titles that depicted peaceful aliens- can you? (Master of Orion wasn't in the same league as Resistance: Fall of Man or teh Haloz.)