After I watched ice shows at KI and Carowinds, where they feature an ice-skating Scooby Doo, I kind of assumed they'd be keeping that license, and using Scooby Doo as the mascot of the former Paramount parks. Nickelodeon, we knew, was going to leave the parks at some point (especially after they started working on the Mall of America stuff), but the HB characters could have co-existed with Snoopy, or stood alone in the parks... which I kind of thought would happen.
From the Wiki page for HB, it seems like Warner Bros. absorbed the studio, and Turner owns these franchises. So the HB stuff is all muddled up with different ownerships. I'm sure that's a big factor with Cedar Fair... they clearly want to improve/update the kid's areas in these parks (and they'd have to, with the Nick license expiring). Having the Snoopy license simplifies things, whereas there may be other contract clauses they have to deal with as there are new owners on both sides.
Keep in mind, Warner Bros. does have ties to Six Flags (not that there's much substance there, besides at SF St. Louis and SF Great America). I would imagine that they want a contract to use a franchise exclusively in CF's theme/amusement parks in the US (I know Universal Studios has a license for walk-around Scooby Doo characters, and Six Flags New England has them in the park parade... plus perhaps even the Jellystone/Yogi campgrounds came into play in this, since CF does own a couple campgrounds). But this is all just speculation on my part.
All of Hanna Barbera is owned by Time Warner now. Turner is just a part of Warner. Any way this past season during Halloween, Kings island used old H-B characters instead of Nick ones for the whole month. So basically they had George Jetson, Astro, Yogi Bear, Dino, Fred, and Barney.
P.S.
King Dominion still has some Hanna Barbera left in Kidsville.