I too find the shoe take off thing disgusting. I haven't raised much of a fuss about it, though I do mumble how gross it is while waiting for them to come out of the x ray.
I tend to take them off at the very last second, I don't take them off well far back in the line like the sheeple.
Also, if the xray is far from the wtmd, I do sometimes mention this is disgusting to the TSO, in a nice way. The more they get the message, the more the slight possibility this unsanitary practice will end.