Personally, (as an American) I have always tipped on the total of the bill. The way printed receipts are laid out, this seems to be encouraged because the big number at the bottom will be the total, with the line under that for writing the tip (presumably based on the total right above it). I don't think there's a nefarious scheme to get you to tip more so much as it's just easier to look at the big number at the bottom rather than try to pick out the pre-tax subtotal (in smaller numbers, a couple of lines further up), and whoever designed the automatic tip suggestion did the same thing: grabbed the total, not the subtotal.
But as everyone says in the comments, this is all just a suggestion anyway.
Personally, though, I err on the side of "too high", especially if it's a restaurant I frequent. My reasoning is this: if I go out to eat twice a week = 104 times a year and if I tip $2 extra each and every time that's $208/year. Eating out 104 times per year and $2 extra is surely well above average but even so, $208/year is not going to lead to my early retirement or a vacation home in Tahiti so really why sweat it. It'll probably make some server slightly happier and costs me little enough to not matter in the long run. I think it's kind of a "penny-wise, dollar-foolish" concept. Plan hard for big investments like your house, your car, your retirement fund, etc, and don't worry over much about a little extra on a tip, is my personal philosophy. I typically tip 20%, and round up to the nearest dollar, because shaving off an extra 32 cents or whatever here and there is really not worth the bother.