NOTE: This answer is no longer valid as of 5.5.3!
See https://stackoverflow.com/a/43205887/1251127
Original answer below.
Currently, MySQL does not offer statistics on index usage.
One way to generate those stats on your own would be to log all queries (Be careful of the extra i/o here) and parse it out. Percona has a nice tool for this, pt-index-usage.