... the amount of allowed transactions included per block is limited. That means that micro-transactions will either not get processed. Or they will need to include an unreasonably high amount of fees
If and when the fees get too high for micropayments to be efficiently handled in the block chain, they can be handled in some kind of sub-ledger. Eventually I think we will see not just micropayments, but also nanopayments - very tiny payments attached to things as small as a single API call.
For now, micropayments and nanopayments can be tested on the block chain, then hived off into a sub-ledger in the future as and when required.