I might sound stupid for this but i would like to know how to disable the player use of speed, fly, noclip all that stuff
For the list of rules that can go in a motd see the list in the "Host one for yourself" page. (Link is on servers page)
For example, to disable fly by default, change Motd in the server software's config/settings gui to "-fly".
If you wanted to only disable noclip on one map (in MCGalaxy), type /map motd -noclip