Many reasons.
1) In back to backs, Holtby played harder teams than Sammy.
2) The team protected Sammy while hanging Holts out to dry on a regular basis--they flat out admitted this more than once because they knew that Holtby would win games for them, keeping them in it long enough that they could come back and get the win. *Which they did a lot, they had more 3rd period come back wins than any other team.
3) Sammy being new, the league/coaches (players, goalie coaches, etc.) didn't have as much tape on him and so didn't know his moves, once they did as the season progressed, Sammy's numbers started dipping.
4) In the majority of games played, Holtby faced a higher degree of high-danger shots (he was #4 in the league of high danger shots faced) and more shots period than Sammy did.
All of that is why Sammy had better numbers than Holtby. Now, let me be clear, Samsonov is a great goalie. I'm thrilled that the Caps have him and he is the future in the net for DC. (The Caps, after all, are my #1 team. Obviously with Holtby now with the Canucks, they are now my #2 team which is weird for me as I've only ever had one hockey team. I have two now. But where Holtby goes, so do I. He's my favorite hockey player. I got into hockey because of him.) However, Holtby has gotten a very raw deal in terms of stats and such with how people view him. Basically, Ovechkin has carried the Caps to success on the offensive end over the last several years and that shows itself in goals. Holtby has carried the team to success on the defensive end over the last several years. Unfortunately, that has shown itself in decreasing numbers in his stats because it means that the defensive core is relying on their final line of defense (the goaltender) to stop the puck way, way too often. And he's been doing it.
The defensive core of the Capitals have relied on their goaltender to win games for them. Period. Because he's done it over and over again. He keeps them in the games, barraged with pucks, high-danger shots left and right (for the last 4 years running, I believe, he's been in the top 3-4 most high-danger shots a goalie has faced) and he keeps them at 3 goals or so which hurts *HIS* stats, but keeps them in the game. And then, now and then, one more puck gets through in the final minute because it's 6 men on the ice, or another crazy barrage. So despite what he's done during the game, it looks like, 'oh, there's Braden Holtby letting in 4 goals again.' But you watch the game and it's a different story. That's been the Washington Capitals' defense for the last four to five years.
I love goalies, but man, it does suck being a fan of goalies sometimes.