Because they don't believe its a fault on their manufacturing issues?
This is only a design flaw if failure is occurring that shouldn't under normal operating conditions. Otherwise its simply a design limitation, and design limitations exist in every product created or that will be created.
If its a design limitation and not a design flaw, then its entirely possible Apple came up with a different/better design that was less susceptible to this in the later 6s line. That doesn't mean the previous design was a flaw.
Those who are lambasting Apple about charging for a design "flaw" are putting the cart ahead of the horse, first you have to prove the design WAS flawed, that failures are occurring within normal usage Apple clearly believes thats not true, they are, in fact, offering a discounted price for fixing something that, at least according to their announced position, is due to user caused abuse of the device. You can believe its a flaw, you can present an argument that its a flaw but its not factually certain that it is, and acting as if anyone who disagrees with you has ignored your argument/is being a blind fanboy, makes you look worse, not them.
Provide your evidence, plead your case, and if Apple continues behaving in a way you disapprove of take your business elsewhere.