Does protection from a specific color help against an ability that cost a different color to activate?
Player A cannot target the creature with Zacama's ability.

It doesn't matter what the ability costs; abilities themselves do not have colors.

What matters for protection is what the source of the ability is, and the source of the ability here is Zacama, Primal Calamity. Because Zacama, Primal Calamity costs Red, Green, and White to cast, it is a Red creature, a Green creature, and a White creature. So Player B's creature has protection from Zacama, which includes all of Zacama's abilities.