I think if you have armies as follows:
Code:
c AAA
c AAA
c AAA
c AAA
where commadners are as far back as possible, and armies as far foraward, they will never attack commanders. at least as long as I've been playing they've never attacked commanders like that. I think there is some sort of algorithm where they attack the closest group to them, unless there is another group within a given distance behind them, then they'll target them, unless there is a group within a give distance behind them too.
as follows
Code:
c
c AA
c A A AA
c AA
c
so here they would see the front army. then the next army is close enough to them they would jump to them, but then the next check shows there is another army close behind them so they would go for them instead. then another check says "hey, there's another set of units behind them!" so they go for them now. That set of units happens to be the commander.
that seems to me to be how it works. I've never seem them jump to attack units or commanders in the rear seperated by a large distance. If it works the way llama said then distance would be irrelevant, and only the number of units between front and back would matter, but I've never experienced flyers jumping straight to the very back like that.