I think most of us agree with the concept--- someone who intrudes onto another's space should pay more--- but there's no practical way to implement it. Imagine the fun of boarding if everyone's got to sit in the Test Chair on the way in and be charged additional fees if they don't pass. Imagine the gateside drama! And what about long-legged people whose knees push into your back? Should they pay more too? The same concept of "intruding into my space" and "reducing my comfort" apply, and it's a logical next step for the airlines to take. The seemingly random enforcement of the two-seat rule is annoying, and no passenger should have to be inconvenienced, but I can definitely think of worse ways to implement and enforce a policy.
What I personally find more annoying, though, is the spread-legged men whose thighs and knees definitely protrude even though they're not heavy-set; just a guy who wants to sit with his legs splayed wide apart. It's not classy when you;re not in a plane, and god forbid you do it in shorts, so there's no reason to do it in the close quarters of a plane. I can cut the heavy folks some slack; it can take a while to get fit, and in the mean time, you've got to go on a plane. But the selfish leg-splaying dudes who have no problem making themselves more comfortable by making me less comfortable, well, those are the ones I really can't stand sitting next to.