While I haven't used the Atari (though I do know that it didn't have memory protection, either,) I've used DOS, Win3.1, classic Mac OS, and Amiga Workbench (1.3 & 3.1.) Honestly, I'd put them all about on par in terms of stability. None of them had memory protection, so one errant process could potentially take down the whole system. Only the Amiga had pre-emptive multi-tasking, so an ill-behaved process could stall out the system almost as easily as a crashy one on Windows and Mac OS. And all three GUI OSes seem to have crashes about as frequently (not terribly often, but it definitely does happen.)
Really, it seems to come down to the quality of the applications you're using, as none of the OSes really have any way to protect themselves from an ill-behaved application. Part of the perception with the Amiga, though, might be because so much software was regularily run off floppies - one or two undetected disk errors can absolutely kill a program's reliability, so the gradual decay of a poorly-manufactured floppy can make software act a lot more unstable than it really is. With Windows and Mac, on the other hand, hard disks were pretty much a given by the time they got well-established.
Really, crazily enough, if you want stability in older computers, you just can't beat DOS. One application has absolute control of the system, with no others to get in its way (barring those pesky TSRs,) and you don't have to worry about any other programs being taken down if it does crash. Of course, that's because there aren't any other programs, due to the whole "no multitasking" thing, but hey! Stability's stability - which is why you'll still find ancient DOS boxes chugging away in the back room of countless little shops when Mac and Windows systems have long since been retired and replaced.
