Trigger script does not work

The code hides some issues that are not obvious unless you indent your code properly.

Let's have a look with an indented version of your code (it does the same thing).

 #pragma strict

 var taps = 0; 
 var tapNow = false;

 function OnTriggerEnter (other : Collider) {
     if(other.tag == "Player") // Test only branches for one statement.
         GameObject.Find( "First Person Controller" ).GetComponent(FPSInputController).enabled = false;
         
     GameObject.Find( "First Person Controller" ).GetComponent(CharacterMotor).enabled = false;
     tapNow = true;
 }

 function Activate () {
     if(tapNow == true); // Wrongly placed ;-sign
     
     if(Input.GetKeyDown("i")) 
         taps = taps + 1;

     if(taps == 50); // Wrongly placed ;-sign
     
     GameObject.Find( "First Person Controller" ).GetComponent(FPSInputController).enabled = true;
     GameObject.Find( "First Person Controller" ).GetComponent( CharacterMotor).enabled = true;
 }

There are a couple of issues that may cause problems. For one, you don't use bodies for your if-statements so you are only executing the next line of code if the condition is met, and the other lines are executed regardless.

Your if-statements in Activate have statement terminators ; which basically render the tests useless.

Here is a version that hopefully works better. As you see, I added bracers around the code in the test, forming a block of code. I also made a small refactoring (extracted a method for enabling or disabling the objects scripts).

 #pragma strict

 var taps = 0; 
 var tapNow = false;

 function OnTriggerEnter (other : Collider) {
     if(other.tag == "Player") 
     {
         EnableFirstPersonController(false);
         tapNow = true;
     }
 }

 function Activate () {
     if(tapNow && Input.GetKeyDown("i"))
     { 
         taps = taps + 1;
         if(taps == 50)
         {
             EnableFirstPersonController(true);
             tapNow = false;
         }
     }
 }
 
 function EnableFirstPersonController(state : boolean) {
     var fpsController = GameObject.Find( "First Person Controller" );
     fpsController.GetComponent(FPSInputController).enabled = state;
     fpsController.GetComponent(CharacterMotor).enabled = state;
 }