The only time Marking doesn't make sense thematically is when you're describing it wrong. If you describe it as someone taunting you, cursing your father, whatever, then that won't work in every situation. Personally, I think that Marking isn't necessarily something the Fighter actively does- it's just something that happens because the Fighter is such a badass.
In other words, a Fighter is able to Mark simply because he's so determined to take down a particular foe (or foes) that his mere presence tells that foe that if they turn their back, by trying to move away or even just by attacking someone else, the Fighter is going to use that opportunity to whack at him. The evil bad guy isn't necessarily choosing to attack the Fighter because he's afraid of him, or because the Fighter made him so angry that he's tricked into doing something foolish, it's because he knows- game mechanics aside- that if he attacks the Rogue, the Fighter's going to get a free hit, and if he attacks the Fighter, nobody's going to get a free hit.