I know running works the whole leg but are the main muscles used your quads?

The main muscles used would be the whole leg, exactly as you said. The leg moves a number of bones in a variety of ways during a running stride, there is no "main muscle) that does this, it requires many muscles working together.

those are the largest muscle groups in your legs and do the most work

Yes. glutes and calves get used a lot too. run in the sand and your calves get sore. run uphill and your glutes get sore. (or is the other way around?)