From the user's perspective, Readability is a subscription service(one that uses pay-what-you-want, but the default is five dollars per month--far from 'micro') and Flattr is a form of donation(notice that it is completely voluntary, unless I am misreading what flattr actually does). Neither are actually micropayments. Both subscription and donation were mentioned in that very Clay Shirky article.

The closest thing to micropayments that has had any success whatsoever have been pay-what-you-want like Radiohead's In Rainbows and the Humble Indie Bundles and even there they get most of their money from the small segment that pays a lot, effectively as a form of donation that subsidizes the people who wish to only pay $0.01(or in Radiohead's case $0)

I have come to my conclusion in 2011 the same way Clay Shirky did in 2003: the trails of dead micropayment services.