I've just started keeping guinea pigs in the past few months and have been reading everything I can get my hands on...most books/articles discourage putting them together, since one accidental kick from the rabbit can break bones, and as smaloney mentioned there are bacteria one animal may carry with no problems while it proves to be lethal for the other. They also have slightly different dietary requirements - while it seems rabbits do fine on guinea pig food, it's not the 'best' for them.
I'm no expert and still filtering through all the biased stuff I'm reading, there seems to be plenty of people who have kept them together with no problems. There is SOME risk of things going badly, but then again I'm keeping three GP boars and risking the odd chance that they may not get along when they're older. Just use good judgement and all should be well
