You are probably to the bike shop and back already, but one thing I would suggest is putting in tire liners, heavy-duty tubes, and get them slimed. May seem like overkill, but after having 4 flats in the same number of weeks, I feel it is totally worthwhile!

My commute is 6 miles roundtrip, too... 3 miles down (on the way to work) and... well, the opposite on the way home. I ride a Trek hybrid that I bought in 1999 and is still going strong. I can't imagine using my road bike to commute, as I commute in work clothes (or at least carry trousers or a skirt and ride in a pair of regular shorts).

Funny how people still think it's "amazing" that I ride to work. It takes me less time to ride my bike than it would to drive, find parking, and walk to my office (not to mention the other many bennies!).