Thanks for your replies chaps.
FireflyBob, I understand what your saying about limiting runways and that in such cases getting airborne would very often be the safest course of action.
My orginal question was only considering a very long runway with no obstacles. If it's totally possible to safely stop all the way up to Vr, I still don't get why I should be forced to take an aeroplane which may be filling with smoke into the air if I don't really need to.