This is particularly relevant since one of the main reasons we're worried about the ad model at all is because it threatens the internet's decentralized nature. Replacing this with a model where you only make payments inside a few centralized organizations would not address this core issue.
That process won't scale to a whole bunch of random, disparate sites especially if you're not heavily invested into them. If you come across a cool blog post and want to tip a bit of money, you'll have to go through the same process, which is just not worth it. And that's before getting into transaction costs!
There have been various services that tried to fix them, but none so far that are convenient and ubiquitous enough to change things. And we really need change: this is, to a large extent, a social problem more than anything. The most important piece for moving away from ads is to make small payment expected and, for lack of a better phrase, socially accepted.
We already have this for small physical goods: it's easy to imagine buying a piece of gum or a magazine at a random newspaper stand. But a similarly small purchase online is both less convenient and less accepted, so it ends up being much less likely. That's the core problem.
http://lesswrong.com/lw/f1/beware_trivial_inconveniences/
Think about this for a second. The human longing for freedom of information is a terrible and wonderful thing. It delineates a pivotal difference between mental emancipation and slavery. It has launched protests, rebellions, and revolutions. Thousands have devoted their lives to it, thousands of others have even died for it. And it can be stopped dead in its tracks by requiring people to search for "how to set up proxy" before viewing their anti-government website.
No, you can click on a button and get a redirect to Paypal, where you then enter your Paypal password and hit "confirm".
Paypal's whole business model is based around making transactions like this convenient and easy (for the payer).
You may as well say that the inconvenience of opening a bank account is too much baggage for people to use Paypal, except pretty much everyone who wants to use Paypal already has a bank account.
You are correct that trying to get users to put CC details in to pay a "microtransaction" will put people off, but there are plenty of convenient (two - three click) payment processes that already have huge amounts of users.
Micropayments are a problem, but as long as you buy a few dollars worth of reddit gold it is more akin to buying a gift card than a micropayment.
The psychological issues are valid, but I'm not seeing technological issues in this specific case.
Some site I've never been to before asks pretty please for 40 cents and I'm not about to go find my wallet (probably in my room across the house) grab my credit card and enter a ton of personal information into some strange form who's security I don't really trust, especially when I know the credit card processor is probably keeping 30c + 3%.
PayPal and similar help but then... I have to use paypal. If only I could just directly send the money (like bitcoin, from me to some address) with a token that the site provided me attached. Pretty sure a lot of people are working in this area to make it happen. I really think app-store ease of transactions with the open web will change things up for the better.
As much as us geeks would love it to be, this is not a technical problem. This is a social/marketing problem.