Actually, if the roots are filling the pot and circling around the bottom, you should gently rip or cut the bottom roots off and spread the remaining roots a bit when you transplant many vegetables, including peppers and tomatoes. It actually stimulates the plant to make more roots. Peppers, like tomatoes, can be planted deeper in the new pot to encourage more rooting. Of course you don't want to remove more than one fourth or so of the roots.

I think as beginners, for some reason we get this idea that plant roots must never be disturbed and any disturbance is very bad. However, usually there's not much to worry about, especially if you're not bare-rooting and seriously messing with them. While some plants are very sensitive to root disturbances, most aren't *really* sensitive, and you'd have to be pretty brutal with them to cause any real problems by removing roots alone.

So you probably didn't do anything life-threatening to your peppers. I'd be a little more worried about watering heavily immediately after repotting than whatever root damage you did. In general, you make fungal problems more likely if you "water in" after a repot--they're a bit more susceptible to pathogens if roots are damaged and haven't had time to callous over when you water (it's essentially an open wound with microorganisms being pressed into it, not all of which will play nice if they get into the wound).

Depends somewhat on the potting medium and on conditions though. If it's very hot, I'd err on the side of watering too soon rather than too late.

To add another reason, watering doesn't generally do a plant as much good until it's had a chance to heal and re-grow the fine root hairs that are the basis of water uptake from soil (those are extensions of individual plant cells and more easily damaged by shifting of soil and arguably a bigger problem than a chunk of root fibers, if enough of them are damaged).

As Ohiofem said, losing roots usually works to stimulate root growth--a response in a healthy plant to compensate for the loss. If the plant isn't healthy enough to grow more roots, the other option is to lose some leaves to balance things out (which isn't anything to worry about provided it's only some of the leaves).

With peppers, I find they don't mind a bit of drought stress, so in future repots, you might hold off on watering until they just begin to wilt--give them maximum recovery time. Just keep them out of the sun if you can to reduce water loss.

[Anybody feel free to correct me anywhere you think I'm wrong, I think I'm really only just coming to understand this stuff I'm typing, and it's late :]

-Bryan