If it is cheaper for them to head to a third city first instead of directly just have the prices reflect it so it is x to layover and y to destination which is less than z a direct flight - if it is even offered.
It does seem like a breakdown in their pricing logic rather than anything injurious the passenger did.
Regular internet is frequently more expensive than the same speed internet + basic cable.
I've done it occasionally on shopping sites.
Product A - $48 Shipping - $10
Free shipping for orders over $50.
So I'll pick a random $2 item that I don't want and save $8 on the final price.
Like, obviously they'd prefer to fill the NY -> SF jet with high ticket price customers, but if there are seats leftover, it's still better to fill them with people making lower cost connections to elsewhere than to have them be empty. And if they need to get those people to Tahoe or wherever anyway, then putting them on that plane may also be preferable to putting the last few NY -> SF ticket on fire sale and undermining the usual higher price.