two things:

1. you should increase $tot, instead of assigning it the current value of $hash{$siteID}
2. you should print $tot outside the while; also, try adding a newline; that would visualise what happens now

In code:

 while (<F>)
 {
  ($siteID, $siteAge, $siteDistance) = (split/,/)[0,1];
  $hash{$siteID} += $siteAge;
  $tot += $siteAge;
 }
 print $tot, "\n";
[download]

Hope that helps :)