You may be able to use NULL-terminated arguments:

find /mnt/media/ -name '*.epub' -print0 |
    rsync -as --files-from=- --from0 --no-relative / /home/user/Documents/ebooks

Or if you don't have that option, try this slightly less comprehensive solution:

find /mnt/media/ -name '*.epub' |
    rsync -as --files-from=- --no-relative / /home/user/Documents/ebooks

You may be able to use NULL-terminated arguments:

find /mnt/media/ -name '*.epub' -print0 |
    rsync -as --files-from=- --from0 --no-relative / /home/user/Documents/ebooks

Or if your find is POSIX and doesn't have the -print0 option, try this slightly less comprehensive solution:

find /mnt/media/ -name '*.epub' |
    rsync -as --files-from=- --no-relative / /home/user/Documents/ebooks