Turnpikes can be a pain, but can also help provide highways in areas that need them but are too expensive to operate/construct without guaranteed revenue. As long as 100% of the toll revenue is going to the operation of the turnpike, there shouldn't be any issue. If there is a profit from the toll road, it should be going in to upgrade the road.
A couple things that annoy me about the turnpike...
1) Lack of exits. Yes it is meant to be a quick trip across the Northern part of the state. However, a major interstate that bisects the metro area has less than a half dozen exits with in it. Not to mention it is missing key interchanges like I-475 and The Trail.
2) Non-Uniform Speed Limit. Time to get away from slow speeds for Trucks, which I think are still 65. Restrict trucks to the right lanes only, but speed them up.
3) Outdated ticket system. Get rid of it. There is no reason to have them anymore. Redo the exits of the turnpike to put in a more uniform toll system.
I really like the system we have here in Oklahoma (they are in green in the map below). All turnpikes are 75 mph, except for maybe one. No reduced truck speed. They help provide connections to areas that didn't have any interstates originally built (for the most part). The funds are kept by the OTA and are used for complete operation and upgrades of the turnpikes. The toll system is simplified with the PikePass electronic readers. There is no slowing down for toll booths. PikePass users have a bypass lane or are able to remain in the left lane and maintain speed.
The tolls aren't terrible. If you are going across state from Missouri to Texas it is about $18 total if memory serves correctly. One of the other turnpikes, the Kilpatrick, which provides an outer North loop through North and West OKC is about $2 for the entire trip. They have central toll booths that charge the fee. If you get off at an exit early you pay at the exit (usually exact change readers) and if you get off just after the toll booth before the end you get a refund.
It would be nice of I-80/90 in the Toledo area would take on a form like that to encourage using it as another means to get across town. Instead you are severely limited in your choices and restricted to mainly surface streets to get around going East or West.