You can't change what's already done so it doesn't do any good feeling guilty about it. Going forward, do some research so you can be well-informed when facing maintenance and repair decisions.
Your 2001 4runner has the 3.4L V6, which has a timing belt instead of a chain. Timing chains are virtually maintenance-free but belts have a recommended replacement interval. For the 3.4, it should be replaced every 90,000 miles. It's not something you can determine in an inspection. It should just be replaced at the interval. If you have maintenance records for the vehicle, you can determine if the replacement was really needed or not. If no records were available, it's a good idea to replace the timing belt and start fresh. You don't want to belt to break.
As for the rotors, they can be machined a time or two to correct for wobbly braking (caused by brake over-heating) but then they'll get too thin to be machined and need to be replaced. Replacing rotors is a possible job to do yourself with parts from the auto parts store. Auto parts stores will also machine rotors that have gotten wobbly (warped). There are instructional items that show you how to remove and re-install the rotors on Youtube, etc.
I don't know exactly what was addressed in the repair but it may be a fair price at a service shop. I prefer to research items myself though and learn how to perform some of them at home. You learn a lot more about the vehicle that way and save a lot of money.
There's nothing wrong with maintaining and older vehicle and keeping it a while (I still maintain and drive my 1985 4runner), and the 3rd-generation 4runner is a great platform, but it helps to become more of an authority on your vehicle so that you know what it needs or doesn't need and can perform much of the maintenance/repairs yourself.