The San Francisco 49ers most definitely deserve to be in the Super Bowl this year. They have a great team. They outplayed the Atlanta Falcons and showed that they are the best team in the NFC this year. They were close last year and got better this year. The 49ers deserve to play for a championship.
It was a very close and exciting game, but the 49ers were able to come from behind and exploit some mistakes to take the lead. Isn't that how this game works? It's not just about who has the best players, all things being equal. It's also about who can take advantage of the weaknesses of the other team. The 49ers did that beautifully.
I suppose the obvious answer is that, yes, they won the games to get in, so they are the NFC team that deserves to be there. Beyond, they have one of the league's best defenses, and a young productive quarterback. Their running game is also one of the best, and they have one of the league's smartest coaches. They deserve to be there as much as any team.
Whether or not a team deserves to get there really has no bearing on anything. The best team to get there is the team that will make it to the Super Bowl. The 49ers were the best team in their division, then their conference, and they made it to the big game with hard work.