I have not interviewed the coaches, but I have a few guesses as to why they went with the Bulldog over the Aggie.
Coaches tend to value experience.
Football coaches are well known for their preference for experience. You can see it in the way that veterans sometimes get perks that freshmen don't. When looking at the top guys in the league, they might have simply gone with the senior over the sophomore.
Of course, this only goes so far. Manziel is ahead of senior third teamer A.J. McCarron.
Murray is the better passer of the two.
While there are a few coaches in the league from the new school of offense, the majority of them have more old school sensibilities. If you consider passing to be the primary job of the quarterback, then the nod goes to the Georgia man. In 2012, Murray had more yards and ten more touchdowns on fewer pass attempts than Manziel did, and his passing efficiency was much higher.
Of course, this only goes so far. Manziel led the league in rushing, and he's not a bad passer by any stretch.
Murray is about to set all kinds of records.
If he stays healthy, Murray will scribble his name all over the SEC record book this fall. This vote could be more of a lifetime achievement award than a true All-SEC vote.
Manziel has eligibility questions.
It's entirely possible that the coaches bumped Manziel down a spot because of his lingering eligibility questions. Coaches might consider this preseason team predictive, e.g. that they expect the first teamers to have the best seasons. No one likes his or her predictions to be wrong, so picking Murray might be a hedge against Manziel potentially not playing the season.
It also might be their attempt to send a message to their players about staying on the NCAA's good side. Bumping Manziel down a spot on a meaningless, symbolic list wouldn't be much of a penalty, but hey, it's something.
They just didn't care.
I'm putting most of my money on this one.
Remember back in 2009 when there was a furor over Tim Tebow not being the unanimous preseason first team quarterback? It turns out that Steve Spurrier was the guy who didn't have Tebow first. Was this some kind of jab at his old school? A protest against Florida not having a pocket passer? Nope. It was basically indifference to the voting process:
Spurrier explained that his director of football operations had filled out the ballot and brought it in to him. Spurrier said he glanced at it, signed off on it, and then realized his mistake much later.
These coaches don't make these votes (or their Coaches' Poll votes either, for that matter). Someone else does it, they sign off on it, and they go back to things that are actually important.
I would imagine that coaches might be asked about who they voted first team quarterback over the coming days, as there was essentially a full-scale inquisition over the missing Tebow vote in 2009. Those who did vote Manziel first will say they don't know why everyone else didn't, and those who voted Murray first will either BS an answer or confess to only glancing at their ballots as Spurrier did four years ago.
Ultimately, this is about as silly as a controversy gets. Fortunately, the actual games kick off in just a week.
Updated: Senator Blutarsky has another pretty entertaining theory too.