The problem isn't so much security. You're right that a properly secure network is just as secure. In fact, when we put our systems in, we install them with physically segmented networks, we put in real firewalls with deep packet inspection, intrusion detection, etc etc... we lock the server down with Bit9 (which runs off of our server rather than Bit9's, so that recent breach wouldn't have affected us) and Antivirus.. we don't connect the unused jacks to the switch.. etc etc.
Despite all of this that we do to make it secure, I have lost track of the number of times we have come back not even a month later to find someone plugged a personal PC loaded with all kinds of junk on it, without even anti-virus, onto our network. So, yeah, nothing infected the Micros server, but at the same time, you just created a hole through your computer into the Micros network. Bad bad bad server! These days everyone know that 'oh, if I plug into that box with flashing lights I can get on the internet'. That is where the real problem I've seen comes in. The owner has done everything right; the idiot employees opened the doors.
And oh god.. the owners/managers with kids who think that they are computer wizards because they can program.. or know the basics of networking.. or even just know how to plug in and turn on a router.. they are the worst. They come in and screw EVERYTHING up without really understanding the big picture.
So yes.. I generally agree with you, and if I were running my own place (god forbid) I would do it with integrated processing and call it a day. But I'm also fairly confident I can MAINTAIN that PCI Compliancy, while most people wouldn't be able to. So while a stand-beside are vulnerable like every other piece of hardware in the world, it is easier to maintain. Most employees know enough to go 'Hey, what the hell are you doing?' if they see someone behind the counter messing with equipment. Most employees don't know enough to realize that 'hey, that guy over in that corner has been here the last five days sniffing our traffic, watching for the pattern'.
Its all a mess though.. even if you're vigilant, someone determined to get in will get in. Its all about making it harder to hack you then it is to hack the guy down the street. Hurts to say that... but its true.