I think it’s what you’re used to. I’m used to the Mac keyboard (since 1994) and I much prefer the command key for keyboard shortcuts. I can use my thumb all day but pressing control with my pinkie starts to hurt really quickly!
You could map Cmd to Ctrl but that only fixes copy/paste, but now it will send a SIGTERM to the terminal on Cmd-C now, which means that’s still a pain.
You could write some custom keyboard driver that intelligently maps the command keys to the right keys the app expects, dynamically based on some rules, but that sounds horribly brittle and likely unworkable.
Also, on decent keyboards (not necessarily expensive) you can remap the keys anyway.