Drones were unregulated until people started doing stupid stuff. When you have medical airlift helicopters or firefighting aircraft grounded because people are flying quadcopters in the area, nobody should be surprised that the FAA is going to bring the hammer down. Yes, requiring transponders for all or most drones is a blunt instrument, but that's what happens when a some of the flying public are grossly irresponsible. Yes, it's a small minority, but it has a serious impact.
Here are just a few links to stories about firefighting aircraft grounded by drones. You can find lots more plus plenty of medevac aircraft stories with a simple Google search.
So yeah, there are relatively few stories of drone strikes on aircraft, but there are all kinds of incidents where they cause havoc without ever touching another aircraft.