I usually estimate how long it will take me to do the job, multiply that by my rate and give the customer a quote on what the job will cost. I do have a minimum figure in my head for certain work (I have a minimum figure for just dropping a tree, another minimum if I have to climb, etc. etc.)
As time goes on I'm getting better at my estimating. I find that tree work is not like construction where you can actually lose money (or work for nothing) if your quote is off. I usually work with my wife, or with one other guy & I have very little overhead. I have found that with trees, I always make money, just on some days it is more than others and on good days it is a lot more.
I'm fortunate to usually be doing the work when the customer is not around (I perfer it that way). They have agreed on a price and are quite happy when they return to find their tree gone and the area cleaner than when they left. If the customer is there and I get the job done quickly, I'll casually make a comment about having good (and expensive) equipment makes the job go quicker.
The only time I would charge an hourly rate would be if I was doing chipping service and I charge a minimum plus every hour after that. Time is on my watch and not the machine's clock.