Yes you can use well water to fill your swimming pool with as there's really no difference than using the water from a city supply or from your well water supply.
The water all either comes from the ground through water wells or from lakes, streams etc and it will not harm your swimming pool or yourself to use well water in your swimming pool.
I used to live out in the country as a kid and we always used well water to fill our swimming pool and never had any problems doing so.
With the well water you get the water free except for the electricity used to pump the water up from the well but that is not very costly.