If you are riding in the same wind the rest of us are around here, the level of effort for your 3 mile commute has the feel of a ten mile commute (see thread Wind on the CO Front Range)! That wind is making us all tired! I'm betting, as others have suggested, that your seat is low and that you may be mashing rather than spinning. I would have LBS (Wheat Ridge Cyclery?) look at seat height. I wouldn't think, however, that a complete head-to-toe fit would be necessary for a 3 mile commute.

Stay after it...it will get better. The day will soon come where you'll be unhappy if you have to be off your bike for some reason.