Digikey pricing is designed around it. They give some really serious volume discounts: they'll happily charge $0.10 / unit when you're buying 1 while charging $0.002 / unit when you're buying a whole reel of 10.000. Similarly, they charge a $7 reeling fee if you don't want cut tape.

Combine that with a stupidly efficient order picking process, and I wouldn't be surprised if they basically break even on small orders.

You've got to remember that those small one-off orders are almost always for industrial prototyping. You don't need to make a lot of money selling 5 units for a hand-assembled prototype when you know you will be selling them 500 units for the initial automated run, or even 50.000 units for the final production run.

Additionally, there's a lot of value in being a one-stop-shop: they might not make a lot of money on small-quantity low-volume items, but if an engineer can purchase their entire BOM from you at once, she is unlikely to go looking for a competitor to save a few bucks on the higher-margin items.