Why don't my modifier keys work anymore?

You mean that you press, say, Command-C and instead of Copy, it types the letter "c"?

Check System Settings->Keyboard, click "Keyboard Shortcuts", then click "Modifiers". What do you see? If it says "No Action" next to the modifiers, that would result in the behavior described above...

Under keyboard, do you have a keyboard menu you can check?

If you do, then Show Keyboard Viewer from that menu.

And verify the modifier keys are getting responses on the computer. If they are not, then you may have a mechanical issue with the keyboard. Sometimes the Num Lock key or Scroll Lock can be activated and cause a problem. Clicking on those keys may deactivate the problem. Most keyboards do not behave that way, but some may have that from being used primarily in the PC world.

Look at your Keyboard settings. The Use F1, F2 keyboard as standard function keys in the Apple menu -> System Settings for keyboard will affect whether or not an FN modifier key is necessary for the keyboard shortcut to work.