About 11 years ago I remember seeing a VHS movie about some kids and their dad who made a crazy flying car. The car helped the man rescue his kids from an evil dungeon. I think the dad worked in a candy factory, too. I was about four or five, so I don't remember much about it, but I recall watching it many times because I loved it. It wasn't a cartoon.
Many of those details match the 1968 musical Chitty Chitty Bang Bang. It involves a flying car, the father is an inventor who creates a new type of candy, and the children are captured by the evil Child Catcher and imprisoned.