Yes, I think that their decision is based on profit, and to be honest, I like it the way that it is set up.
Usually, when my family goes to Cedar Point (except for last year when we went in the fall) we stay at Camper Village. We buy one ticket for Cedar Point. Then we buy one ticket the next day for Soak City. It is cheaper to do this than it is to buy two tickets for Cedar Point or a two day ticket. I think that it is nice to be able to go to Soak City without paying for the entire amusement park.
In addition, I think that having seperate prices adds more to the resort feel of Cedar Point. And Cedar Point has enough rides and attractions to fill up a whole day. I can't see visiting Cedar Point for one day and having time to visit the water park too.
Be thankful, many parks put their Challenge Park type rides inside the park itself. That way, you have to pay to get into the park and then pay more to go on a Ripcord type attraction or go-karts. At least with this set up, resort guests (or anyone else) can run over and ride the go-karts without paying the entire park entrance fee.
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...and enjoy the rest of your day at Cedar Point, The Am-aaaa-zement park!