Is it safe to delete the innodb schema on a new Amazon RDS instance?
There is a reason you cannot touch the innodb database.

This is where Amazon stores the system tablespace file ibdata1

If you run 

SHOW GLOBAL VARIABLES LIKE 'innodb_data_home_dir';


you might see something like this

/rdsdbdata/db/innodb


It will point to this folder as the base of InnoDB.

If you run

SHOW GLOBAL VARIABLES LIKE 'innodb_log_group_home_dir';


you might see something like this

/rdsdbdata/log/innodb


This is where ib_logfile0 and ib_logfile1 live.

If you run

use innodb
show tables;


you will see nothing because there are no .frm files in it.

Even though the innodb database contains no storage engine data files (.frm or .ibd), you cannot drop the innodb database because the folder /rdsdbdata/db/innodb is not empty.