Three reasons:
1. forging
2. heat-treat
3. steel choice
My custom fixed blades are beauties, fully-forged, differentially heat-treated 52100 or other fantastic carbon steel. There are no knife companies that do that because they can't efficiently, quickly, and cheaply do that using the labor of technicians on an assembly line. Only a skilled knife smith can do that. Go ahead and check, no factory is using 52100, none of them are differentially heat-treating, and none of them are forging blades. It takes too much time and is too expensive for them.
What are the advantages? Well, finer grain structure in the steel, better performance of the better steel, and better toughness/edge-retention dynamic. Were talking about peak-performance. That's if you care that much about the performance. Frankly, a cheap Buck will actually probably be fine for most hunting and woods tasks. Hell, I've got a Cold Steel Pendleton Lite Hunter ($15 knife) and it does just fine for most stuff. Some of us just think custom made knives are cool. We also desire/like the beauty, tradition, and peace-of-mind that comes with hand-made craftsmanship. Oh, and very importantly: we are willing to pay the moolah.
I agree with you that some factory knives are overpriced, imho. If a company is charging $300 for a knife made on an assembly line, I'd much rather give that to a skilled knife smith. But that said, I'm talking about the kind of custom knife I mentioned above. Basically, a knife that a factory can't make. Other kinds of knives... I'd just go with the factory up to a certain price point because they can quickly and reliably address warranty/refund/replacement/repair issues. I dont think Id be willing to pay someone over $100 to get a totally-average blank, grind and sharpen it a bit, slap scales on, and then send it across the country to be heat-treated. Thats just my personal feeling because I fail to see what they are offering thats special. ALSO, a custom knife maker can make anything you can describe to him, if it is makeable. Factories generally won't do that.
Cheers,
Mag