TokuDB optimize table does not reclaim disk space
I've had the same experience. The solution is to rebuild the table via this command:

ALTER TABLE my_table ENGINE=TokuDB ROW_FORMAT=TOKUDB_SMALL;


Replace TOKUDB_SMALL with your favourite compression algorithm.

With InnoDB an OPTIMIZE TABLE command simply does a trivial ALTER. But in TokuDB it does not, and tablespace is not reclaimed. By forcing an ALTER with ENGINE=TOKUDB you're taking this outside TokuDB's hands, and let the MySQL server tell TokuDB to create a (really) new table.