Why not? I've used milled PCBs for commercial prototypes as they're an order of magnitude cheaper than a fab given the turnaround time. You can get down to 0.5mm pitch easily.
You don't get soldermasks and vias are normally riveted (good enough). For most people, two layers is enough and if you can design the board well you shouldn't need much routing on the second layer.
Without a soldermask, how do you mount anything SMD finer than about a SOT-23? (only a slight exaggeration)
I can't imagine mounting even a simple ATTiny, let alone a quad-flat anything or a bunch of 0603s without a solder mask.
I'm sure that some use cases can get by with all DIP, through-hole, and similar-sized parts, but it's hard to design a product that can later scale up cost-effectively without being able to use surface-mount parts. There's a reason the mass production all switched over to SMD->cost.
Remember there are plenty of companies who need the odd PCB, but aren't in the PCB business.
Simple power/control boards (weird voltage, multiple outputs) that aren't available off the shelf from RS or Farnell. None of those boards need to be more than two layers. I've designed lens focus control boards that only required a single layer.
Yes of course if you're doing RF or fast serial you'd be daft to do it on a milled board, but they are convenient sometimes.
In the UK, you're looking at ~£50 for a short turnaround from a fab house like PCBTrain. From there a single small two-layer board, 50x60mm, 15 weekday turnaround is £33 plus shipping . It scales very well, but that's not the point for a prototype. Want that board this week? £90. Oshpark is great, but only if you can afford to wait the 20 or so days it takes to get to you.
If anyone can recommend a good, cheap fab house in the UK I'd be interested to know about it!
Perfboard is fine up to a point, but I find it tends to get messy, even for simple boards, and it's not terribly optimal with regard to space. You're out of luck (without bodging) if any component is surface mount or isn't 2.54mm pitch.
Milling is a nice stopgap when you need a single copy of a board that's a bit too complicated for perfboard (i.e. different pitch/smt parts) but isn't worth spending 10x the cost for a professionally made board. With milled boards you can have custom shapes, cutouts and so on. If you're trying to design a board to fit inside some housing with a funny shape and standoff points, milling the board to fit is a nice and cheap.
You don't get soldermasks and vias are normally riveted (good enough). For most people, two layers is enough and if you can design the board well you shouldn't need much routing on the second layer.