Bigger isn't actually bigger.
I think you will find that Colgan is NOT larger than CommutAir, and definitely no more stable.
Although the Colgan website claims to have 15 aircraft, the number I heard when I interviewed with them two months ago was more like 12... They dumped half their Saabs after 9/11 and furloughed a bunch of pilots, and many ran away as fast as they could. If I am not mistaken, and I may very well be, CommutAir is running 16 airplanes right now.
I never worked for Colgan, but I'll tell you what, the overall impression I had of the company was far from positive. Subsequent conversations with former Colgan pilots only served to reinforce that impression. They didn't offer me a job, which was fine by me, I wouldn't have gone there even if the pay were better... To say nothing of the prospect of flying ten year-old C-model 1900's, which comprise at least half of their fleet.
CommutAir on the other hand... Well I left there over six months ago, and it was a torturous decision on my part. I didn't really want to leave, but the situation at that time and the offer(s) I had to go elsewhere led me to walk out the door. I can recommend them with the only caveat being that they do have a cloud hanging over their head in the form of a lawsuit brought against them by senior pilots who suspected some fraud in the ESOP program, and if the company LOSES that lawsuit, who KNOWS what would happen? People I know who are still there are doing a lot of flying and say the loads are picking up, so it sounds like the working environment is still pretty good.
All in all, CommutAir was a great place to work and I think they are a MUCH better choice than Colgan. Furthermore, if CommutAir's situation continues to improve, you can probably look forward to a fairly rapid upgrade.