Why Are Proofs Generally Less Valued In Resale Markets?

This is not how it works. Proof sets are minted to demand, so the lower mintages are because people are buying less sets. Newer proof sets have more coins in them (Native American Dollar, ATB Quarters, Presidential dollars, etc.) than the older sets do, thus the issue price is higher.

Here is an older collectors idea on all of this.
When I was a kid, communications were not as instantaneous as today. Getting a new coin for the album meant either making a trip to the local coin shop (if you had one - urban areas only), finding one in change, or waiting a whole month for the next issue of your favorite coin magazine so you could check the lists and mail order them. We won't mention Littleton.

The hobby was mainly all about the anticipation of hunting for and thrill of finding (you hoped) hole fillers from change/circulation. Regular issue coins is what it was all about. And since there was no eBay-instantaneous-buy-it-now full collection of (let's say) Franklin half dollars at your cell-phone-dancing-fingertips 24/7, the hunt to complete your album/set was what it was all about for most people.

Plus the makers of those "little holes" rarely ever included (if at all) holes for proof issues. Why were no proof issues included in the albums? Again, the mindset seemed more to be that a "complete set" was made of "regular coins" anyone had a chance of finding in circulation. Since proofs were just the mint showing how perfect they could make a coin, proofs were not normal coins and certainly were just extras not to be confused with being a part of the "actual" (album-hole-defined) set.

Had Whitman made holes for proofs, things may have been different. But, then again, maybe not. Some other company may have become dominant that "knew" it was taboo to break coins out of a proof set (more on this later).

Think of typical car - normal coins. Think of curb feelers on a car (dating myself) - proof coins - not standard issue.

Just like an awful lot of collectors are afraid to crack a coin out of a slab, back in those days no one would be crazy enough to break apart an officially packaged, "US Government Mint Proof Set." After all, the marketers made sure we were aware proofs were incredibly special coins being of the highest possible quality, and (a big point here) no human hand had ever touched them! A handled proof coin violated this no-touchy rule and stripped the coin of its sacred status/value. Proofs were a world apart from what went into our "complete" album sets.

Another point is proofs lacked the fundamental thing which keeps hobbies alive: the thrill of the hunt to bag something special. Anyone could have a proof by throwing money at them, however not everyone had found a 1932-S quarter...yet!

I think the old stigma of proof coins only being a sideline special issue kept the prices low when the internet appeared. As the newer generation has come along, they see tons of proofs online for very little money. Hence the lower mintage eye candy coins are seen as having no real value to them.

Albums with proof holes are more well known now, but the vast majority still don't have those holes. So except for a few special sets for eye candy, few people still want the proofs.

Admittedly the idea that a complete set is one from regular issue coins (with a few exceptions) is so deeply ingrained in me that I don't go after proofs. I make an exception on Ikes and Kennedy halves simply b/c, for some reason, I just want them.

Two super, thoughtful posts by earle and conder on this topic.

Earle and Conder, thank you so much for your very thoughtful answers, they make total sense. It's not every day you get a fully satisfying explanation for something, and so I'm really glad I finally got around to asking this!

They have no soul! Even the mint state coins seem sterile to me. No one's used them for anything, they haven't survived. The AUs hold the most interest to me: they generally look nice but that little bit of wear means that they've been in a few pockets and bought a few things. They've been part of the world.

Well, scarcity plays a part in all this - the proofs are not generally all that scarce.

Yes, @Silver81, I did not want to say this out loud, but coin collecting itself is not particularly rational, assuming that I or anyone care. We can't be stopped. Logic does not apply. Mr. Spock and the other Vulcans could not become coin collectors.