I would imagine that this is a common issue around the world. You get on a bus and they need you to store your baggage under the bus because of course it would be impractical to have everyone sitting in their seats with gigantic backpacks on their laps. Of course you could try to do this, but someone is probably going to have an issue with it especially if you are a solo traveler.
I first encountered the reason why people are and should be apprehensive to put their bags under the bus / coach when I was in Thailand back in the early 2000's and while it didn't happen to me, it did happen to someone that I befriended upon our arrival in what I think was Phuket.
Bus travel over long distances is dying out in Thailand due to the emergence of low cost airlines but there was a time when your only real inexpensive option for travel was to get on a long-haul bus on coaches that promised some level of luxury that of course they were all lying about. They were incredibly cheap and this appealed to a lot of the backpacker types back in those days when budget airlines didn't really exist. Back in those days Thailand had only a few airlines and they were all "full-service" ones that meant a bus journey was going to cost 1/10 the price. A lot of folks, including me, opted for the bus instead of flying after talking to a tour agent (remember those days?)
So what happens is that when you get on these buses, you sit up top while all the cargo goes under the bus. Just look at the above image and see how far off the ground you really are. Now look at where the driver is sitting. The heightened elevation for passengers is exclusively because this vessel is a cargo transport as well as a person transport. From my experience these buses also functioned as parcel delivery mechanisms first, and the people were just an added bonus.
All manner of things are being transported on your journey and this gear doesn't necessarily belong to people that are on the bus. This is just how they make some extra money. Where things get a bit dodgy is when the cargo storage area is accessible by the people that are on the bus and if you are on a double decker bus, that is almost certainly what you are dealing with.
In my situation all of our gear except for our very important items such as passports and cash were stored on our person in either a bum bag or a daypack. I had a small backpack that had my camera, cash, cards, and other things I considered important.
For someone that I met on this trip and ended up hanging out with, she had left a lot of this gear in her backpack that was below decks and it wasn't until we had arrived at our destination that she realized she had been done over.
When we arrived in Phuket (again, I am not certain if this was our actual destination) the luggage crew was hustling everyone along as they tend to do in these countries because smaller buses were awaiting to take us to various parts of the city. Myself and everyone else in my "crew" at the time, thought nothing of this and hurried on our way.
It wasn't until we arrived at our guesthouse and checked in that the one girl realized that there were many items missing from the backpack that she had stowed under the bus. Someone had rifled through her stuff while we were sleeping on the bus and then carefully rearranged the items in her bag so that she wouldn't notice until much later.
In total they got a bunch of cash, some jewelry, some cards, and a camera. When we tried to contact the bus company of course everyone pleaded innocent and even though she got very angry with them, there wasn't really anything that could be done. It now is evident to me why they were hustling us to our onward buses even though we ended up sitting for a while waiting for said bus to depart. They knew that if they kept us moving we would not have a chance to check our belongings until we were already gone.
Now, this situation of course is the fault of the girl who left these valuables in an unattended bag in the first place and I am quite certain that she would never make this mistake again but I learned something that day: Do NOT leave anything that is valuable in your bag under the bus. I didn't just because I am generally an untrusting person in the first place but she had some sort of weird faith in the people that were running the bus system.
I remember at the time that she was in tears and that the total loss for her was around $1000. The police of course were useless and the bus company tried to claim that she was lying. The police were not on her side and what are they going to do even if they were? Search the house of all the baggage collectors who were on that bus that day?
I don't think that anyone would do this these days but one very important thing to keep in mind when you are budget traveling is that in exchange for reduced prices on just about everything you are also going to be submitting yourself to a far lower level of accountability and security. This is not to suggest that budget travel is dangerous but a certain level of common sense needs to be applied to these situations.
If you can not see your bags assume they will be rummaged through. They can not steal your entire bag of course because you would notice that. They also can not tear open your bag because you will notice that right away as well.
At the bare minimum I think that all backpackers need to keep their valuables on their person in a bus and perhaps put locks on their bags below. I would imagine that the thieves look for the easiest bags to break into and if you put just a little bit of precaution in their way they will likely move on.