How high above the finished floor is the top of the flange? Ideally, it should be flush to maybe 1/4" higher than the floor.

If it is significantly higher and is indeed limiting the ability of your toilet to sit flush on the floor, then the best option is to replace the flange. With PVC or ABS it's fairly easy. If cast iron, call in a plumber.

While to me it's a misplaced "repair", I've seen people with tall flanges build up the area under the toilet, essentially raising the entire toilet up an inch or so. While it solves the problem, it doesn't really solve the problem. It just creates a new one.

If it's just an uneven floor that's causing the rocking, or an out-of-flat toilet base that's causing the rocking, I like to use plastic shims to level the base and prevent the toilet from wobbling. Then I'll caulk the gap around the base of the toilet, but leave an inch or so in the back uncaulked. That way if you ever had a leak under the toilet, you'd know about it, instead of the caulk holding the water in, sight unseen, while damage occurred.

I don't recommend plumbers putty, especially if you have a stone floor.

Thanks for the answer. It is probably more than 1/4" It is the height of the flange which is a little more than that probably. It is not a metal flange. So for the future...do flanges come in different heights? So we could have gotten a "flatter" one? Sorry, I have never installed a toilet before. So, the problem is not an uneven floor...it is just that the flange was entirely above the tile floor instead of sitting down. So, the toilet is in and it is an elongated so it actually came to the floor in the front but not the back so he has a piece of cardboard under the front until he caulks. Now he has to cut the bolts off for the caps to fit on - is that normal. Thanks for your patience with my very basic questions.

Flanges are slightly different sizes, but the height is usually set by cutting the pipe that mates to the flange a certain distance below the subfloor.

When the flange is plumbed, usually there's just the subfloor in place. So you'd add the thickness of the underlayment (if any) to the thickness of the finish flooring, and that's how high above the subfloor you want the toilet flange to be.

It's common for a plumber to add a 1/4" or so to that, most prefer the flange to be slightly above the finish flooring than to end up below it.

Knowing how high you want the flange above the subfloor, you then cut the waste pipe at the appropriate spot so when it's glued together the flange sits at the proper elevation.

If the flange truly sits too high, the best thing to do is cut the waste pipe down and set a new flange. The flange can be cut out from the inside of the pipe, I have a small round blade, about 2" in diameter, that's on a shaft about 12" long. I mount it in a drill, insert it down the pipe, and cut the pipe from the inside.

It's not uncommon for the flange bolts to be too long and to have to cut them down to get the caps to fit. That's not a big deal.

So...long flange bolts? Not a problem.

The flange set so high that the toilet rocks when set upon it? That's bad. I wouldn't accept that. You don't want your wax ring to be crushed to nothing, you'll lose your seal. I'd have the flange reset.