For me it's because they're so often used in an exploitative way. I'll use gaming again as my example. Look at Farmville, or what seems like the majority of mobile games lately. It's so common to see "Pay $2 for mojo points" or whatever their pretend currency may be, and used to sell virtual items. Now that in itself isn't evil, but these items are often things to make the game less "grindy", and so developers are encouraged to add grind in the first place to maximize profit. The developer isn't focusing on making the best possible experience for the player anymore.

That's true mostly with Farmville (buy a tractor to double your harvest speed), but other games take this on as well too. Another example: Companies want to sell over-priced map packs and such, and so will stop the modding communities from creating their own content. If there aren't user submitted maps the company can sell their own for far more.

I used games as an example because it's the easiest for me to come up with examples, but I think this extends into other mediums as well. To me, micropayments change the focus of the publisher of that medium to look for profit where they didn't before, and that creates a worse product.

This is a very loose idea I've had in my head for a while and I haven't put it all together like this before, I'm certainly not an expert on business models or anything like that. This post is purely conjecture on my part.