Gate-checking does put the stroller in the hold, but it goes on TOP of the baggage that comes from the bag room. That means that there is less opportunity for damage due to being crushed, but it doesn't mean that there is no opportunity for damage at all. Also, if you read the fine print on your gate-check tag, you will notice that signing it absolves the airline from responsibility for damage.
I've actually questioned ramp workers on this topic, and to a man, they told me that the usual reason that strollers get broken is that they come unfolded while they are being moved. These guys just grab the thing; and if they happen to hit the fold latch, they don't have time to study it and figure out how to properly re-latch it. They will cram it flat any old way that they can, and they WILL use brute force to do it. It is up to you to do what you can to make sure that this doesn't accidentally happen; at very least use a strap or bungee to make sure it stays folded, at best, put a padded water-resistant cover sleeve on it.
As for damage to cup holders, napper bars, canopies, etc., that is not unexpected. Automated equipment *is* used to move gate-checked luggage, and anything that sticks out can get caught in it. Again, be proactive: remove the canopy, napper bar, cupholders, pouches, etc., and put them inside one of your checked bags for the trip.
That said, I've always taken these steps when I checked my strollers, and the only time I've had one damaged during a trip, it was my own fault, or actually, DS' fault. We were in our gate area waiting for a delayed flight, and he got out of his stroller and walked right between Mom's legs, causing me to trip and fall. In avoiding falling on the baby, I fell on the stroller -- unfortunately, I'm not built like Kate Moss, and I bent the frame.
I used a ripstop sleeve to protect my stroller when checked; it leaves the wheels and handle exposed so that it can be pulled down the jetway. My SOP was to wrap my empty backpack carseat satchel around the body of the stroller inside the sleeve; both padding it and eliminating the need to find a place to store the satchel whilst in flight.