Most gamers are aware of how Valve became so big and it's through the modding community in HL1 and eventually HL2. Can you imagine how prohibitive it would have been for Counter-Strike to grow if they charged $10 for the mod (obviously when it was till a mod =< v1.6)?
On top of that, some mods were genuine improvements over the original. For instance, there is a huge Skyrim UI mod that is a vast improvement over the vanilla. Some people were actually afraid that game companies would use this pay for mod system as a way to double dip. "Let's release a half-assed UI, let some modder charge for his better UI and take 45-50% of his sales."