I personally think it's a great system (although personally I would prefer a less intrusive email, followed up by a phone call only if the customer doesn't click on "accept" or "look for different choices").
There are probably lots of people who would panic when they get to the airport and find their (old) flight number no longer listed.
But yeah, no matter what they do, somebody will whine about it -- the trick for a service provider is to find the system that will get the least amount of whining, knowing that it cannot be eliminated!