Ugh I have the same thing happening. I haven't figured out a solution and Ive been hru all the setting. On my iPhone Im only showing my iCloud synced calendar and it is also the default calendar for making appts. I still show all my calendars in notification center. I think its a design issue. Is there a way to notify apple of this issue?
I don't think it is possible in the current OS. I have tried everything I could think of and had no luck. Hopefully it is something that will be fixed in .1 or so.