Welcome to FT!

To the check-in agent at LAX your destination was ZRH/Switzerland. You had no valid Schengen visa, hence you were not allowed travel. The agent would have violated Swiss/Schengen immigration law by allowing you to travel without a Schengen visa regardless that you had a separate ticket from ZRH and promissing to stay in transit at ZRH. What if you had cancelled the ZRH-IST flight after the agent had checked you in to ZRH?

If it is of any consolation to you, this is a very common mistake when travel on separate ticket. But there is nothing else to do, than move on.

As for rebooking you need to contact Aeroplan for refund or rebooking of the LAX-ZRH ticket (you should state that you were not able to travel due having no visa for Switzerland) and contact TK M&S for refund or rebooking of the ZRH-IST ticket (you will need to pay a USD 70 refund/change fee for this).