| That'll happen. It takes a while for the butt to toughen up if you haven't been in the saddle for awhile. Most of us feel a little bit of that every spring, even if we've been putting in our trainer time in the basement.
Seat covers won't help, because they only make the seat wider and result in more friction. Friction is your enemy.
Just about any standard padded cycle shorts WILL help.
Seat height might have contributed to the problem. It should be high enough that your leg is almost straight, but not so high that your hips rock while pedaling. You can't always tell if its right by yourself. Your instructor should have stood behind you to watch your hips. The determining factor here is flexibility of your hamstrings. Most people end up with just a slight kneebend on the downstroke. Some of the less flexible require more of a bend.
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