The only time I price by the hour is when I am working for a friend (usually at a reduced rate). I tell them I can give them a price that will probably be a little high, but if it is OK with them, I'll just charge by the hour. "Regular" clients want a final price.
Or more importance though, I think charging by the hour is asking for sticker shock. When you tell them your per hour rate is $65, $75, $85 or whatever, the will think "gosh...I only make $20 per hour". Many people don't associate the other direct per hour costs to an employer (workers comp, social security), let alone the other fixed costs to employ somebody (for example, maybe, health insurance and vacation days)... That doesn't even touch on the fact that you have equipment to pay for, fuel to buy, etc... PLUS, most of us have to make the bulk of our living in 9 or 10 months instead of all 12. No...I just don't think many people will understand all of the things that go into a "high" per hour rate.
Like Todd aluded to: stick to the contract. If something changes, get it in writing (change the original contract, and have both parties initial the change) unless you are willing to take the loss of not getting paid for the change. That would have taken care of your example regardless of how it was priced. Based on what you have said: I am pretty sure they could have only paid you for the time it took to take down 6 trees...you would have lost in court unless the contract said "all marked trees". From your description if sounds like it said "6 trees to be marked". If you didn't have a contract (assuming the total job was over $500), you definately would have not had a case in court.