Deeply hidden T's and C's

Booked a flight to Germany via ebookers with Austrian Airlines and Lufthansa. I unfortunately could not make the one flight from Berlin-Vienna-Hamburg. One week later I then had my flight back home from Hamburg to Johannesburg. When I tried to check-in my reference/booking code could not be found. I had to go to the airport only to find out that my entire international flight back home was cancelled because I missed the one flight a week ago. I would have to pay a 3000 euro fee if I would want to get back on the same flight. No communication on this at all from airline or Ebookers! This info is nowhere to be found on the itinerary, their website or the airlines websites. Was forced to buy another ticket back home at the last minute. Totally unacceptable as a flight booking agency to not communicate this.

Apparently this is common practice for Airlines to do this? But if you're booking through a flight agency or third party website how do you as the customer know this if they do not clearly highlight this or bring it to your attention? How is it also ok for an airline to completely cancel a flight that has already been paid for without letting you as a customer or the know? Saying that it's part of the T's and C's (which is also not upfront) is definitely not a good enough answer.