Why were the 49ers out-coached by the Rams?

This is a mix of a rhetorical question and a question actually looking for an answer. While there is plenty of blame to be mixed in for poor execution, there just seemed to be something incredibly off with the coaching staff in this game. It is easy to get into an argument over subjective things like what we think of the play-calling, there is more to this than just those subjective discussions:

Harbaugh admits bad play call on zone-read option pitch. Also, players said Rams were in perfect defense for everything 49ers had called.

— Matt Maiocco (@MaioccoCSN) December 2, 2012

Even if you remove the absurdity of calling the read option deep in their own territory, all indications are this was not a good game for the 49ers coaching staff. Jeff Fisher seemed to take at least a little bit of pleasure in the Rams victory

Dig this: #Rams coach Jeff Fisher on the #49ers botched read option: "I don't know what they were trying to accomplish there."

— Eric Branch (@Eric_Branch) December 3, 2012

Fisher's Rams now sits 1-0-1 against the 49ers and 4-0-1 against the division as a whole. It's a small sample size and there is a lot of football left to be played, but he's certainly off to a good start.

Is this Fisher being that good, the 49ers coaching staff getting a little over-confident at times, or something else entirely? I really don't know what to make of this at this point. Sometimes it seems like the coaching staff gets too cute, other times it's like they out-smart themselves. I just don't know what to make of it and wanted to open the floor for discussion.