If you haven't already, bind the Control modifier to your Caps Lock key. Emacs was developed on workstations with this key configuration, and a lot of key combinations make more sense for your fingers that way.
If you've already done that, I wouldn't worry too much -- there are plenty of programmers working now who've been using Emacs for more than 20 years.
If you use the Caps Lock key as CTRL, then it feels pretty awkward for me to type some key combinations (like ctrl-x or ctrl-c) and still keep my fingers on the "home row".
Do you just get used to this? Do you type ctrl-x with your pinky and ring finger? Or, do you shift your hand away from the home row and type ctrl-x with your pinky and middle finger?
Ran across this long after the fact, and I'm not even sure if you'll be aware I posted this, but...
I've been wondering the same thing, as C-x is used all the time and seems really uncomfortable. I've found one mention of it, so I thought I'd pass along Steve Yegge's opinion:
"Incidentally, if you want to fine-tune this tip to extraordinary levels, then you probably don't want to use your ring-finger for typing the x-key when you hit Ctrl-x. I use my left index finger, since I'm used to it that way, but you're probably better off using your left middle finger. The reason is that your hand isn't technically on home row when your left pinkie is jammed down on the Caps-Lock key that you've turned into Ctrl. The point is to use whatever requires the least amount of stretching, followed by the least amount of finger motion. You should experiment until you find what's most comfortable for you."
If you've already done that, I wouldn't worry too much -- there are plenty of programmers working now who've been using Emacs for more than 20 years.