When you finish your ride (both ends) spend five to twenty minutes stretching. Do it slowly, don't bounce (it's not how far you go, it's how long you hold plus how many repetitions). Stretch your hamstrings and calf muscles. Stretch your quads (something like a laid-back hurdler's stretch). Do it slowly, hold 15-60 seconds, release and repeat. Do it before you cool down, then go clean up and get on with whatever you were doing. If you can, stretch at other points in the day as well.

It may also help if you make a point of warming up slowly over the first few miles and warming down at the end. Get the blood flowing before you put big loads on the muscles.

Keep your cadence high (95-110 rpm) and you may find that the leg pain stops. If you are a lugger with a low cadence, you'll have to work up to a higher spin. Just do it for a few minutes a couple of times each ride until you can last longer. It will eventually become natural to ride at a higher cadence, which will increase your endurance.

I also agree with Walter S. If you're driving on the days you don't ride and if you can leave your car at work, consider doing something like driving in one day with your bike, then riding home and back in the next day. Then drive back home and do your round-trip thing the next day.