With your listed airports it looks like Southwest would be the airline that serves both cities with the most flights. Second choice looks to be Delta or American. I would suggest reading up on the Rapid Rewards threads on this forum and ask some questions there. Given your level of flying you might not be in a position to gain status with any one airline just yet unless you were prepared for a couple of mileage runs or if you take a long trip each year.

I do know that Rapid Rewards has some interesting earning rules and the expiration of credits can be a problem. I have not flown SWA for years, but I do remember losing out on a "free" flight with them because of their rules. The Southwest people on this site will know much more about this.