The number of protons are not suppose to be equal to the number of electrons? How come we are subtracting them from each other and getting a value? Did I miss something here?

You must be referring to some work related to ions.

Ions are charged particles which can be formed when atoms either gain or lose electrons.

Metallic elements will lose electrons and become positively charged.

Example
A sodium atom has 11protons and 11 electrons
A sodium ion (+1) has 11 protons and only 10 electrons
The ions has a +1 charge because it lost 1 electron (when you substract a negative the result is positive)

Aluminum has 13 protons and 13electrons
The aluminum ion (+3) forms after three electrons are lost, still 13 protons but now only 10 electrons

Non-metallic elements gain electrons when forming ions and will have negative charges

Fluorine has 9 protons and 9 electrons
A ${F}^{-}$ ion has 9 protons and 10 electrons, note the ion will now be called a Fluoride ion