How do you cook calamari / squid and avoid making it tough?
Calamari or squid is of course famous for being difficult to cook, because it gets tough or rubbery.

As Harold McGee explains in On Food and Cooking, octopus and squid meat are very rich in collagen:


  They are chewy when lightly cooked, tough when cooked to the
  denaturing temperatures of their collagen, around 120 - 130 F / 50 -
  55 C, and become tender with long, slow cooking.


The trick then is to either:


Cook them minimally, so they do not begin to toughen.  This Serious Eats recipe for fried calamari recommends no more than one minute.  

My own interpretation of this is that it will keep the temperature of the squid below the 120 F threshold, at the risk of being below the pathogen kill point, so it should be done only with squid from a trustworthy purveyor.
Cook them for a long time, slowly, as in a braise, so they move through the tough phase to tender again.  This Food Network recipe  for stuffed squid by Ann Burrell is an example.  The total squid cooking time is 20 to 25 minutes.