We cannot measure the absolute value of energy of a Bohr orbit as mentioned by you.We can measure only the relative energy with respect to a fixed reference.In this case we fix our reference to the electron at an infinite distance (by infinite distance I do not mean that the electron is some light years away, it means that the electron is just far away from the influence of the nucleus of the atom) where the energy is assumed to be zero since there is no interaction. Now with respect to this energy level the electrons in the orbits are bound so they have lower energy which should be less than zero (i.e. negative energy as you said)
So the negative sign before the energy has a physical significance which tells us that the electron is bound to nucleus unlike the electron which is free having zero interaction energy.