I think that people haven't yet really got out of the mindset where you couldn't bring your own food on planes. Now that you can, their providing food (or not) is much less of an issue, but it's still hard, for me, at least, to resist the frisson of thinking "free food!" (even if, as you say, I have already more than paid for it).
No, it's not a deal breaker, but it's something small that makes the customer feel valued/appreciated and not like a walking dollar sign whose presence is an annoyance to the flight crew.
And in an industry characterized by extremely low margins a $0.50 bag of peanuts per person is definitely significant money out of their pocket.
Its value is a lot more than 50 cents when you've been hauling a baby through airports, sat on the tarmac because of weather, and didn't have time to grab a scrap of food yourself.
Is this really a selling point? A bag of $0.50 nuts to accompany a $500.00 ticket?