Page 18 of the 4th Edition rulebook states: "The special ability on a dominant is instantaneous and nothing can negate its effect."
The REG clarifies Protect as: "A protect ability allows a card to be unaffected by special abilities or game rules that would normally affect it."
Since Dominants only inherently have CBN status, you are free to protect from them (or, in cases like Judas' Plot and Herod's Temple, instead them).
