I try not to be 'that guy' who goes around bashing companies for fun, but since you asked, I'll tell you that I had the same experience with Thrifty on 3 different occasions at 3 different locations, and have since refused to use the company regardless of cost savings. The long story made short is that Thrifty will bring you in with a cheap price and then do anything and everything they possibly can to 'upsell' you on insurance and other add-ons. In one case, I was asked whether or not I wanted to add the extra insurance for the rental and I said 'No, I don't want any extra insurance.' To this, the agent said, 'ok, so you just want the basic.' It was not until I returned the car that I realized the 'basic' was actually a $30 per day upsell! I am the first to admit that I should have more fully read the contract they had me sign, but I had been very clear about the fact that I didn't want any extra, and they were intentionally subversive to that desire and cost me $240 in the process.
They do tend to have good rates, but be very careful about what you agree to. It is my experience that they find a way to make up the difference in other ways.
With that said, I am a HUGE advocate of the National Emerald Club. Rates are generally competitive and you simply walk out the door, pick out your car and drive out through the window. We've been extremely happy each time we've used them in a number of different locations.