Everyone has to find a fee structure that works for them, their equipment and the client. You have to make money to stay in business and you should know what it actually costs to perform your services.
I have always kept detailed records of the logs I have sawn, how long it took and what the yield was. Using p/bf rates I found that my financial productivity dropped significantly with certain types of logs, primarily those less than 12" in diameter or less than 6' long. The extra handling and clamping time increased considerably compared to the board footage produced - often to to the point that I would have been working for free.
Most of my milling is charged by the board foot. My hourly rate ($60) is only used for 'low productivity' situations - to reduce the liklihood of me working for free, or less. My history as a client of portable mills also led me to be more comfortable with p/bf pricing. I could measure the log and get a pretty close idea of how much it should cost, regardless of the style of mill or sawyer's efficiency.
When I do a site visit I explain the fees to the client and, if it is an hourly job (or part of it is), I explain why and the potential increased cost (on a per board foot comparison) of milling their logs. Most are surprised by how much I can get done in an hour of milling.
Last week I had a mobile job milling walnut. We milled for 8 hours (I hooked up in the dark) and produced over 1900 board feet with 1750 bf of that being 8/4 with widths to 23", much of it clear. Not counting travel, my fee was just under $700 (about $87 p/hr). What did the client get? His local woodworkers store/lumberyard has 4/4 walnut for $4.99 and 8/4 for $7.99 p/bf, + extra for wide widths. The retail value of his lumber would be almost $15,000. Of course, he'll have to wait for it to dry and he may cull a few boards but even at $2 per board foot, hiring a portable sawmill to salvage his logs was a very good investment!