My son was congested from day 1 as well. We have 2 cats (figured that was the problem). Turns out he's allergic to dogs (don't know where that came from) and dust mites. Apparently, the dust mite allergy is pretty common. Try an allergen mattress cover, take any stuffed toys out of the room, vacuum daily, wash sheets in hot, and don't dust unless your LO is out of the room/house for quite a while. You can also try an air purifier, but I've heard mixed results with those. If the problem persists, you may be able to get a low-dose prescription from your doctor to help on bad days (we use Zyrtec when he's really congested).
HTH
Melissa