No, that is not a simple sentence. The simple sentence would be "We went to Six Flags."
Yes, the statement "Today we went to Six Flags, but it rained" is a simple statement. It conveys a single event (going to Six Flags) and the additional information about the weather (rain).
Yes, the statement "Today we went to Six Flags, but it rained" is a simple one. It conveys a single event or situation: going to Six Flags and experiencing rain during the visit.