How do I keep players from accessing certain commands?

By default, the majority of commands (with the exception of /me, /tell, /help, and /trigger for some reason) are restricted to server ops. Players are, by default, not allowed to use any other commands on a server. Server ops can use other commands. You can specify ops in the ops.txt file, or by using the command /op <playername> in the console, or in-game (assuming you have added yourself as an op).

By default, server ops have access to all commands, including commands like /stop. You can change this by modifying the op-permission-level in your server.properties file. Setting it to 4 (which is the default) allows ops to use all commands. Setting it to 3 restricts the /stop command, and setting it to 2 restricts server moderation commands (/kick, /ban, /op, /deop). You can still use all of these commands in the server console.

Adding on to @Unionhawk's answer you could aternatively just use a permissions plugin such as Group Manager or PermissionsEX with Bukkit along with the Essentials plugins. I'd definitely recommend reading some guides on running a Minecraft server, this not the best guide but a guide nonetheless and should point you in the right direction. Just google around to try find a guide that will suit you best in your objective.

there are 3 steps- 1. In order for players to be able to break blocks near spawn, (spawn protection) they must be OP. So OP them.
2. close the server, and open the server.properties file . 3. change the OP permission level to 1. this will restrict all OPs, so they no longer have commands. But, they can still break blocks around spawn.
If you want to run commands, you must run them out of the server console.