The problem is that tipping by percentage is an industry practice. The server has no idea what your intentions were by your tip; all they have to go by is the percentage. If that percentage is low, it may give them the impression that they did something wrong.
And yes, I do completely understand where you're coming from. In many cases the price of a meal doesn't necessarily reflect the quality or type of service you receive, but in other cases it may. In a more high-end restaurant, for example, servers probably have smaller sections (maybe only 3 or 4 tables at a time) to wait on because they have more steps to follow with each table. In that case, they need to maximize their tips. In a more relaxed setting like a bar, a server might have 10-12 tables at a time, so each individual tip doesn't matter as much because they'll all add up a lot quicker.