I think the biggest reason is that because you are ahead by 4, time spent is more of a commodity than time saved. Loosing 40 seconds, means that Seattle has 20 seconds to call 3 plays instead of over 60, more chance for mistakes, more chance to confuse the opponents, more chances that Seattle burns a timeout because they are not ready etc, etc. By calling a timeout, it indirectly sends the message that you are conceding the touchdown, and want to give as much time to Offense to get a field goal. It also lets Seattle look at the defense and plan accordingly, and probably gives them the edge.
The risk obviously is they score on second down, you only have 20 seconds, but 2 timeouts. If they score at 60 seconds, you only have 1 timeout.
At the end he had more faith that the defense would get a stop or two, than his team driving down the field and scoring a field goal.
At the end, the Pats needed a break to go their way (after the Kearse catch), and we have seen last second plays go either way (remember the Sterling Moore past breakup followed by missed field goal?). Odds of fumbling, dropping passes, etc probably are much higher when the game (the ultimate game) is on the line. It worked out, and we call it genius, but I think if he called a time out, then extremely likely Seattle scores.
