In Harley's case, they changed to chains from the gear drives that were standard on their earlier engines because of several factors. One of those was supposedly sound emissions, but the most important to Harley was related to cost. Gear drives require tighter tolerances on all the various parts ($), require more precision in assembly ($), and have much less capability to tolerate failures of the first two requirements (more $ for warranty when they screw up). So the simple answer is, $.
I find it to be very amusing and enlightening when I think about just how many other companies have used chains to drive everything from overhead cams to transaxles and transfer cases for decades, all without the widespread failures and drama of the Twin Cam Harley engines. It still comes down to poor engineering and cheapskate management at H-D. They have a real talent for taking technology that has worked very well elsewhere and somehow screwing it up. And they don't seem to care a whole lot when they do screw the pooch. No extended coverage was ever offered by the factory even when the failure rates became impossible to ignore (but they noticed the trend enough to come up with a kit to change the old system over to the new system on older bikes, and then promoted same through the dealers as a customer paid "upgrade").
Jerry