Classical mechanics doesn't really work to describe how/why two species bond. For instance the positive charges of 2 Hydrogen nuclei should be repelled from each other and therefore you would think that Hydrogen gas should exist as Hydrogen atoms. However, Hydrogen gas exists as 2 Hydrogen atoms sharing a pair of electrons because the configuration of the electrons around the two protons is such that it is of lower energy when the electrons are "shared" then when they are not.
In Chemistry we do not talk about electrons bonding with protons. In Chemistry, a bond is when an ion/atom/molecule "decides" to share electrons with another ion/atom/molecule. The two species will "decide" to bond if the energy of the overall system will decrease by them forming bonds.
There are two main factors involved, entropy and enthalpy, commonly thought of as disorder and heat, respectively. The relation of these factors to energy is known as the Gibbs' Free Energy equation ΔG=ΔH-TΔS (H is enthalpy and S is entropy). In order for a process to proceed spontaneously, you need the ΔG to be negative (all systems tend to the lowest energy state possible).
When two species become one, the entropy of the system (typically) is decreasing making the [-TΔS] term positive. In order to have that process be spontaneous, the ΔH term must be negative enough to overcome the positive TΔS term. Physically this is observed as heat or spark or an explosion or what have you. Now you have a system where covalent bonds were formed and the system is at its lowest energy state. In order to go the other way, you need to put energy back into the system to break those bonds.
The funny thing is, that blanket statements like that tend to be a little misleading. Even if a process is spontaneous (overall negative ΔG), there is a certain amount of energy that you need to put into the system to "get things started." This is called the Activation Energy and is the reason why the wood that is around you right now is not bursting into flames as you read this message.