Don't bother trying. Its an ability and it just works. Trying to rationalize it will give you a headache.
Why does choosing to attack someone else mean you "ignore" the fighter?
If you are being flanked by a rogue but specifically concentrating on fighting him he still gets sneak attack damage so paying attention to an enemy has NO mechanical effect.
The combat boardgame has its own rules that may or may not connect to the rest of the game in any way.
There is no mechanical BENEFIT to saying "I focus on this enemy".
Unless of course there is. Such as a ranger's ability to focus on an enemy as his quarry, or an avenger's ability to focus his oath of enmity onto a single target.
Again, the only mark that needs to be "rationalize" is going to be the fighter since "magic" can cover just about any rule that may or may not connect to the rest of the game and thus doesn't need to be roleplayed.
While, admitedly, the fighter's mark working when they fighter isn't in a position to attack the person again AND the person the fighter has marked being immune to fear might make the mark seem illogical, that is a case of keeping the game simple being more important than having it make sense in every possible corner case. (See also: elimination of undead having character resistance: rogue) In a situation where a fighter is next to the person they have marked, the fighter is continuing to threaten them with their weapon. A fight isn't just "I hit you and then stand and wait until it's my turn again or I get a chance to interupt" ... that is just how it looks to the
players on a macro scale. The fight itself will have a number of parrys, thrusts, feints, etc which accomplish nothing in terms of damage, but for a fighter keeps his enemy from being able to swing at someone else. The same way that anybody is able to punch someone in the face for trying to fire off a ranged/area attack or walk away ... the guy with special training is able to catch subtler tells like swinging against someone other than the fighter, or shifting. And he knows where to hit someone/something to stop it in its tracks.
On your point about ignoring the fighter ... far from it. The mark means that even when you are attacking someone else, you are still focusing on the fighter a little bit ... thus you don't have your full focus on your target and suffer a penalty to the attack. He doesn't get an attack in because you've left yourself open (without the fighter training, he wouldn't have noticed what little opening you did give), but instead he's reinforcing the threats he's making. As for what causes the mark ... -2 is the same as cover or concealment. If the fighter is right next to you, he could easily be doing things to you which just as easily cause a similar effect. If nothing else keeping "one eye on the guy that is threatening and taunting you" would have some effect on your vision/focus/etc.
Heck the magical marks have similar implications. Divine Challenge causes the paladin's allies to seem less clear in the eyes of the one who has been challenged, while the paladin is clear as day, for example. The arcane energy of the Aegis pulls subtlely on the enemies weapon as it strikes against the ally, causing it to either miss, or not hit as hard. The warden's connection to the earth allows him to connect to the enemies nearest to him, allowing him to pull them back or strike at them should they dare refuse to respect his threats. Etc ...
Having a single "this is how it works" isn't going to work. With 4e, you either embrace "it's a game, who cares how it works" or you embrace "there is no single right answer, there can be a myriad of ways to flavor the abilities, and it doesn't have to work the same way each time."
