Well, part of it is that even a small payment can still incur a psychologically large cost. If each user post here on /. cost one cent to read, would you want to have them load automatically? Probably not, many of them are not worth that much, and you could quickly run up a bill of a few hundred dollars a year on that sort of thing from this site alone. So instead you'd have to take more time to think about what was worth spending even a little on, because it adds up and the price doesn't really match the value to you of the thing you'd be paying for.
Something similar happens when people have metered or capped Internet usage compared to at least nominally unlimited usage.
You really can't avoid this problem unless the micropayment is so small that it is likely not worth the cost to implement. I suppose if I knew that a year's worth of micro payments for me, for everything I use, was no more than about a dollar a year in total, it wouldn't be so much that it would feel like I was wasting money on the Internet. But because the average user doesn't want to spend a noticeable amount ever, and there really aren't that many users in comparison to sites, the resulting pie of money wouldn't be much to split up. (Especially once you reduce the amount to account for lower average incomes elsewhere in the world)