Mysql: Insert performance INNODB vs MYISAM
The reason is very simple. When you insert a row into MyISAM, it just puts it into the server's memory and hopes that the server will flush it to disk at some point in the future. Good luck if the server crashes.

When you insert a row into InnoDB it syncs the transaction durably to disk, and that requires it to wait for the disk to spin.  Do the math on your system and see how long that takes.

You can improve this by relaxing innodb_flush_log_at_trx_commit or by batching rows within a transaction instead of doing one transaction per row.

I highly recommend reading High Performance MySQL 3rd Edition (I am the author).