To answer this question, I am going to employ two metaphors:
As little children many of us pedaled about on a bicycle equipped with training wheels. Were it not for the training wheels, we would have an unfortunate spill. That day would finally come when, after our legs had become stronger and our core able to balance comfortably, our parents would undo the training wheels and—whoosh!—we’d be off down the road. The training wheels provided us with the necessary practice to ride a bicycle.
As children many of us have seriously injured our legs, be it a twisted ankle or a broken femur. Afterwards, we have to move about on crutches as our legs heal. Crutches are necessary to help our injury heal. Once the cast is off, however, our legs are withered and an act as simple as walking to fridge for some milk becomes very difficult. Indeed, we are tempted to use the crutches, as our ability to move with them is far more efficient than it is as we hobble about on our atrophied limb. Ultimately, we must ditch the crutches in order to recover our ability to walk normally. Otherwise, though we may be consummate crutch walkers, we’ll always move about in a compromised fashion.
The GRE RC Passage
Underlining the passage, or as is the case with the computer-based test taking notes, is an inefficient means of attacking a timed reading passage on the GRE. You may become relatively adept at it, but in doing so you are robbing yourself of a more effective means of doing a passage: active reading. Also, becoming a better note taker does not necessarily make you a better active reader. If anything, the more you rely on the note taking method, the harder it will be to break the habit.
By now, you should be able to tell that underlining/note taking is similar to the crutches. It works, but in a diminished sense, when you compare it to the far more effective active reading. As you guessed, active reading represents the training wheels, and ultimately, when you become adept at it, the bicycle.
Here is a post I wrote for our GMAT blog on active reading. It pertains 100% to the GRE Reading Comprehension. That is, whenever you see GMAT RC passage just substitute GRE RC passage. I highly recommend checking it out for more tips!