And I guess this one could be cuase SE is in the GY when it destroys, but secret samurais protection isnt working either, and Im confused those last ones protection isnt working either
Dunno about this card, but Secret Six Sam's protection doesn't work against Survival's End because Survival's End graveyard effect destroys 2 cards, not just 1 (your opponent's card and your Dino). Secret Six Sam can protect from destruction only if exactly 1 card (and no other) is gonna get destroyed.
I've succesfully used this against cards like double cyclone & treacherous trap hole that targets 2 cards.
It doesn't work because the text reads "negate it and destroy it", Survival's end can't be distroyed if it already is in the graveyard. I know, sounds like total BS but that's how this game works. lol
My comment about only working against destruction to 1 card is a response to the other anon mentioning about Secret Six Sam also not working against Survival End.
Whether the card can be destroyed or not is irrelevant. (You can negate a card like Newdoria or Grave Squirmer with this.) Survival's End's destruction effect is not the activation of a Spell/Trap Card, however.