You are totally fine with asking her to stop. What started out as a favor has turned into an obligation, that's the bottom line. As you said, when she first asked she mentioned getting her own car or changing her work schedule, so there was an implicit agreement that the favor would be temporary. That has obviously changed and you don't wish to be obligated any further. It's wonderful that she has paid for gas and been prompt, that has probably what has led to this favor continuing for far longer than originally intended. She's a great carpool buddy so she should have no problem finding another person to carpool with then. But you just simply don't wish to carpool anymore and want the freedom of being a solo commuter again. Good for you.
I worked with a woman like this. She didn't drive and carpooled with 2 others on a regular basis. She was always on time, bought the driver breakfast, etc. and would alter her schedule to suit the driver. She thought she was the most considerate person and prided herself on being a great carpooler. However, driver1 always confided in me how she dreaded the obligation, that she still lost at least 1/2 an hour a day going out of her way to go home (weird traffic pattern on the PM commute) but she didn't know how to say no. So you are not alone, OP, in feeling as you do. It's hard to turn people down when they aren't 'behaving badly". It really is hard to stand up for yourself so I wish you luck in doing this and getting your commute back!