Six of the nine offensive drives resulted in points. (One of those drives was the end of game/victory kneel down) Only one of those drives ended with a touchdown to Stevie Johnson. This is not new for the team. David Akers was the leading offensive scorer during his tenure with the Niners. In the 2011 season Akers scored a total of 166 points.
There's a great Niners Nation article breaking down the 49ers red zone plays vs. Chiefs that shows where missed blocks and the lack of development in plays, including Kaepernick not always seeing open receivers, have stunted the Niners offense at the end of drives.
Kap, however, is developing through his progressions more this season and adding WR weapons may be a part of it. Crabtree, Boldin, Llyod, Johnson and Patton are a formidable group of weapons not to mention Miller at FB and Davis at TE when he's healthy.
Obviously a win is a win, but to allow teams to stay in the game with a chance at a winning drive is not the optimum situation. The defense can clearly win games for the team, but relying on them to do so shouldn't be the expectation.