Betting "for protection" is not sufficient reason to make a bet or raise in big bet games like it is in limit games when the pot is large compared to the bets going in. Because the bets are so large compared to the pot, the EV aspect of protection is very much overshadowed by your equity against his calling range and what this sets up on future streets.

In response to your 3-bet preflop being for value, I don't think you have sufficient reads or stats on your opponent to conclude that this is +EV compared to calling. Even if we suppose he's calling with 10% of total hands preflop, you're going to be between 51% and 53% ahead preflop, which seems like an edge but it's really not because of the rake and being OOP.

I would like to see you put your opponent on a range on the flop, decide what hands he would bet (or check behind) if you check, and decide what hands he would call (or raise) if you bet, and the same on the turn. I made an awesome picture to help you remember how important this is, which I have put at the top of this message.

Best of luck, and if you have any trouble with this feel free to come by the IRC channel (link in my signature) and we'll help you out.