This tells my you are likely riding on underinflated tires. Are you checking the psi prior to each ride (or at least every morning?) Since this is a road-bike, I'll assume you are riding 700-23 or 700-25. My experience is that every day the bike sits, it loses 10-20 psi until it gets down to 80 or 90 psi and then hovers. The tire still "feels" firm, but it isn't sufficient to hold me (220 lbs) up. If you are checking the inflation and still getting the flats, I'm stumped.

As to flat-resistant tires, I think the armadillos are tougher than the contis, but for a road-bike I much prefer the contis since they are lighter and seem to have better grip in corners. Downside of the contis is that I don't think the sidewall is reinforced with kevlar like the specialized. For a commuter though I recommend the armadillos.