Yes, the AMC shows are somewhat bad examples for the reasons you mention. I'm just using poor shorthand because those are the shows that everyone knows. Thanks for pointing it out.
That said, those AMC shows are all mature shows, that NOW have the associated proven audiences/demos to reach the ad sales they do.
But what about NEW shows? For internally developed OR pickup shows, without the supplementary income of affiliate fees, what would be the incentive for a network to take a risk on a big budget/innovative show and nurture it to GET to the place (and ads) that the AMC shows are now at? If cable networks were only at the whims of the ad spends, they wouldn't shoulder as much risk. Shows that take time to find their footing would killed before they ever had a chance at lifting off. That's why cable is different than broadcast, and it's why (arguably) the best television ever has come from cable. Content aside, pop early Walking Dead or Mad Men on ABC, and after a couple of weeks of sub 2.5s, the show is done. Hell, even ON AMC, all of the aforementioned shows have been squeezed on their production budgets, and that's WITH the affiliate fees and ads coming in!
More than anything, I just think people should know that the problem is FAR more complex than what it's made out to be, in this thread and elsewhere. It's not simply "commercials pay for everything/let me pay only for the stuff I like". It's many interrelated factors and some hard truths.
I know that big conglomerates own many networks. In my mind, that's an argument FOR the affiliate/current model (although there should be ownership limits), and illustrates why the aka-carte model wouldn't work. The rising tide lifts all boats into more choice for the consumer, and more risk taking for the networks (which, ultimately, in my view, benefits the content).
To go back to the poster that mentioned paying $8/month for the 4 networks they like...awesome! Get ready for a world of 10 or so networks, with the rest probably dying out because they didn't reach critical mass, and can't stay in the black. Sure, they have people willing to pay for them...just not enough to keep it running and/or producing the same content/quality level. (It's not "extra" money to the companies, either, because anyone who's now paying $80+ to get a bundle of cable would switch to an $8 plan, too. I don't believe the difference would be made up in volume.)
If people want to pay without bundling, I think the long-term effect would be everything creeping to the boring middle. "Safe" shows, and "safe" networks. Everything niche and different and challenging dies out, because it's too risky, or appeals to too narrow an audience! AMC could've never grown the brand it is today if the ala-carte system were already in place.
To me, the state of the movies are a perfect example of how this can go wrong. It's not a perfect analogy, of course, but most everything is now a sequel or pre-existing property (book adaptations, comics, etc), because it is engineered for max profitability from the beginning, because it relies on direct payment. But, no commercials (well, product placement and tie-ins aside).
Would they ability to pay only for the stuff you like be awesome? Yes, of course!
Could and should cable companies take less off the top? Of COURSE, but good luck with that.
To me, the far more troubling problem is the monopolies/duoopolies that cable/satellite companies have been allowed to establish over entire geographical areas. If we all had 3+ companies competing for our cable dollars and carrying the networks we wanted (even if not ala carte), prices would push down.