It is counter-intuitive...
When you read through the whole procedure for calculating a V1 speed then it makes sense.
You have to go with the book values, otherwise why bothering trying to go fly at all? Is there anything intuitive that suggests hundreds of tons of aircraft should hoist itself off the ground using interaction with tiny molecules of air? Not to me! It works, though.
Think about a slippery runway. You will have trouble stopping, so that you use a low V1 speed because you will have a long accelerate-stop distance. Try to stop moving any faster than V1 and, yes, you will go off the far end, when low speed or high speed you are going to have an accident. Trying to go shouldn't be such a problem, though; the remaining engine or engines get you up to Vr and away you go!
If you are one of nature's pessimists who doesn't trust mechanical devices more than a little, tiny bit then aviation probably isn't for you in the first place. To see what I mean, try looking out the window the next time you are off to someplace or other in a 4-engine airliner to see just how long it takes, how far down the runway you are when that thing finally starts flying. You seriously think it would be a good idea to ignore having passed V1 to stomp on the brakes and hope to stop a 747 or A340 in the little bit of runway left?
No, sorry, it doesn't work that way even if it seems as though it should! If it did then we would all be much safer flying low and slow, eh?