BMW-Welt is indeed free. It is basically a new-car showroom and delivery center on steroids, with a number of interesting exhibits mixed in. Since Rolls-Royce and Mini are part of the BMW corporate family, their products are on display as well. There are places to eat, and a terrific gift shop. You can easily spend an hour or two on BMW-Welt alone, just exploring on your own. It is worth a visit.
The more extensive BMW Museum is across the street, with an admission fee and more limited hours.
The boys will also enjoy the campuses of the Deutsches Museum dedicated to transportation -- Verkehrszentrum (U4 or U5 to Schwanthalerhöhe), covering all manner of surface transportation; and Flugwerft Schleißheim (S1 to Oberschleißheim) for things with wings. Flugwerft is on Germany's oldest operating airfield, in buildings that date back to WW1. Just a short walk away are the colorful Schleißheim Palaces, summer home of the Bavarian royal family.
Photos of BMW-Welt, Verhkehrszentrum and Flugwerft Schleißheim are here.
Note that the main Deutsches Museum campus on Museuminsel has just begun a decade-long renovation project. For the next few years portions of the museum and some major exhibits will be closed. Almost all of the fascinating aircraft normally displayed at the main museum have been moved to Flugwerft.