Bukkit

Is there a way to  limit how many times command can be used in a day based on a permission group?

So let's say default group can only use /rtp 5 times a day

I don't believe per day limiting is possible but you can set a cooldown in the command and define a permission for it and then give that permission to the group with your permission management plugin.

Example for the command with 2h cooldown (cooldown is defined in seconds):

'defaultrtp':
  command: /rspawn
  type: RUN_CONSOLE
  runcmd:
  - /rtp player $player
  - $text$&aWhoosh!
  cooldown: 7200
  register: true
  permission-required: true
  permission-node: mycommand.cmd.defaultrtp

You can do that using the playerdata feature. Check the dailybonus example, and expand it with another condition, who counts how many times the command got used.