When you pull the tube out, pay attention to its orientation. Hook the pump up and find where the air hisses out. Look at the corresponding spot on the tire and find the hole. If it's small (depending on the type of bike/tire we're talking about here) then there's no need to worry about it. Just make sure to feel around on the inside of the tire and make sure no thorns, glass, or other hazards still exist. If you really want, put a tube patch over the hole on the inside of the tire. Then put in a new tube and go. Thorns and small pieces of glass will often work their way through a tire without cutting the threads of the casing, in which case you're fine.
Depending on the road hazards present on the commute and the necessity of on-time arrival, ask your local bike shop for tires that have a puncture protection layer. Specialized Armadillo tires are expensive, but we installed them on a fleet of rickshaws I was managing and cut out over 90% of our puncture flat incidents. At $5 per tube, plus CO2 cartridges for emergency inflation, we figured the the cost difference paid for itself 5 times over during the lifespan of the tires...not to mention lost fares.
Thorn-proof tubes (I used to buy them from performance bike) are made of really thick rubber so they add weight, but are another way to up your protection factor and your fitness level.
Also, if this is a thin road bike tire, they tend to be more prone to hazards working their way through the tread when they get worn down. I used to get about 3000 miles out of flat-resistant training tires when I was a bike-racer guy. When I got my first flat on the road, I knew it was time for a new set of tires.