How do physicians figure the percentage of vision loss for someone with glaucoma?

Complex. Measuring a person's true visual capacity is an incredibly complex and difficult to perform test. A multitude of factors go into achieving good vision and trying to place a percentage on vision loss is simplistic at best. With that being said certain tests like visual field loss, loss of contrast sensitivity, decrease in visual acuity can be surrogates for visual function.
Estimation. Vision can be quantified in many ways, such as on an eye chart, using a visual field test, etc. So the amount of vision loss depends on how it is defined. Typically, someone who has lost a certain amount of peripheral vision due to glaucoma is given that estimated percentage of vision loss.