There's only the one parking lot at IND, and it's very small. The station is unstaffed, and the parking lot will be unpatrolled, so you'll park at your own risk. It's not a bad area of town, though, so I wouldn't worry too much. Just keep valuables with you or locked in the trunk, and you probably won't have any trouble.
Hermann is a wonderful vacation spot. The whole town is walkable, and there are several bed-and-breakfasts, antique shops, wineries, and the like. I would not recommend going on a weekend during Oktoberfest, as that's when the party crowds make a mess of the place. Otherwise, it's a pleasant and stress-free town.