Jill Tarter is right that the science fiction staple of aliens wanting to eat us is virtually guaranteed to be wrong -- to say nothing of Star Trek and its idea that most aliens are basically exaggerated Americans with funny ears or foreheads who can freely interbreed with each other. No, it is very likely that any truly alien life will have major chemical differences from familiar Earth life -- even if that alien life is also based on organic chemistry and water.
That doesn't mean we'd necessarily be safe, though. Aliens who made it to the solar system would see Mars as prime real estate -- nice and empty, all they have to do is move in their furniture and hang some pictures. (That is "terraforming" Mars to make it habitable for them should be no trouble for a species that could travel between stars, and the difficulty of interstellar travel would mean they would want some kind of payoff at the end.) The only downside would be the messy neighbors.
Earth would be too much of a mess for them to want to come here. They may not actually be susceptible to a War of the Worlds-type infection, but the fact that Earth's own life is in every little nook and cranny would make it difficult to establish their own biosphere here, nor would they feel a need to. Just to be on the safe side and keep us from tracking our muddy shoes across their new carpet, though, they might very well nuke us back to the stone age, after which they would make sure we never again achieved space flight.