If someone is protected (for example with Shield) it is like he is not in the game?
Essentially yes, but only when resolving the ignored effect(s). As far as I recall, all protection/ignore cards either ignore all opponents' main effects or allow you to choose which effect to ignore. Other rules (such as if the player has enough VP to win the game, or if the player is in Red Alert) still affect that player.
Also if you only want to consider his/her victory points for executing (main) effects? That would be really counter-intuitive.
If you are ignoring an effect, you ignore all of that effect, including considering/counting your VP if the effect says to do so. Again, the cards that let you ignore effects, ignore opponents' effects, which are usually going to be bad for you. In that case, I don't find it counter-intuitive that the opponent can't use your VP against you when you have Shields up.