About 4 years ago, before WN flew into BOS, I had some award tickets to use and Mrs. Deubster & I flew into MHT, picked up a rental car, and drove the hour south to Boston. At which point we stayed in a Back Bay hotel and parked our car in their garage for 5 days at $28/day (relatively cheap for the area). Didn't take the car out once, partly because Boston is a walking town with decent public transport, and partly because there's no place on the street to park.

Sure, I could have stayed in outlying areas at a hotel with free parking, but it was more than worth it to be in the area, and cheaper than a 1-way rental.

No big deal, if you know in advance and budget for it. If you don't expect it, it can hurt, but I think the lack of a little research on your part is mostly to blame. You've got to expect it in certain cities, and you can always check things out with a phone call.