Tooling waived when re-ordered emphasises what I've said - this is a one off up front cost that you pay before you get any product that can be sold to customers.
Note that I haven't said that PCB manf is hard. I've even said that companies don't do this stuff in house, but that they outsource it.
I'm pretty sure Sunstone doesn't charge for tooling if you use their proprietary software. You're locked in, but the costs aren't too bad for development. I'm sure getting the actual gerbers is a pain. ExpressPCB has a similar deal where they will make three index card size boards for $51 total. Not too bad, but they charge ~$60 for the gerbers.
If you're using "normal" software that can generate gerbers, there are other options. If you don't mind long turnaround and overseas fab, Seeed Studio will make boards for ~$1 each, for 5cmx5cm [1]. Slightly more for larger boards.
For hobby projects and prototypes, OSH Park can't be beat. Started as a board pooling coop for open hardware, they now send out batch jobs a few times a week to Amitron in IL and produce high quality boards (ENIG, with silk screen and soldermask) for $5/in^2 (for three copies, so a 1.5in^2 board would be $3.75 each)[2]. Their ordering process couldn't be better--upload gerbers, approve an on-screen rendering, specify the number of boards, and enter your billing info. No confusing options to go through. Seriously, try it. It's awesome.
So board fab is not that expensive anymore, and perhaps cheaper than when you last looked. The turnaround times aren't great for the inexpensive options, but with luck or good EDA it's possible to get by without too many iterations.
Board fab is over an order of magnitude cheaper than that these days. Yes, I have old circuit boards that I designed 15+ years ago that cost me $400 for two bare PC board prototypes, but today I can get the same two for about $50 these days, shipped express from somewhere in China.
To go even more extreme, I just ordered a handful of an existing design from OSH park just to see what their quality is. Three tiny boards cost me $5. Five bucks!!!
PCB fabrication is the easiest part of shipping hardware.