Hi there! We just actually went to the Jelly Belly Factory over this past weekend. We did not plan it as a special trip, rather were in Wisconsin for another reason and decided to stop on by on our way out of the state.
The other responses were pretty accurate. You sit on a little "train" and drive around the "factory" more like a storage warehouse while you watch how the candy is made on TV screens. The tour lasts about 1/2 hour.
I had my daughter (3 1/2) and son (10 months) with me along with family friends who also had a 3 1/2 year old daughter and 9 month old daughter. All of the kids were fine and enjoyed the ride on the "train." The girls also enjoyed the free candy at the end and the candy store. There were no active play areas for the children, but the staff were great. The adults enjoyed the tour, too.
I'm not sure that I'd plan a trip just to go there, but if you are in the area I'd check it out. Hope this helps!