I've got a minotaur figher who's super AC'ed up (25 right now) and I'm trying to see if the 0,2 weapon of protection is better than the 1,1 weapon of protection. Or if a 2,4-weapon is good enough that it's worth losing the 'of protection'. They're all the same thing, axe, or mace...can't quite remember off the top of my head.
They're all better in different situations. If something is hard to hit, the extra accuracy is better, but if something is easy to hit, the damage is better. I guess if something is both hard to hit and hard to kill the damage would probably be better because then when you hit you you'd have a better chance of killing them. Those numbers (1,1 vs 0,2) aren't really different enough that it'll make much difference though, it's a bigger deal when you're comparing something like (4,2 vs 0,7). As long as you aren't having to rest too often you're probably doing fine. I think there's some damage types that go through AC (smiting?) and if you are fighting those things the pure 2,4 weapon would be better against them since your AC isn't going to do much for you. I try to carry around a few different weapons to switch between as the situation demands it, but it's usually more determined by the brands. Usually you have time to switch while gaps get closed (or you duck around a corner).
If I'm playing a caster than "of protection" is great because I don't expect things to get to close to me very often, or the only things I plan on meleeing are weak things (rats and the like). If I'm playing a melee based character than I want a more offensive brand probably (of freezing, of draining, of fire, vorpal, of electrocution, of poison, of anti-magic) and that's going to depend on what dungeon branch I'm in. Certain areas have more characters vulnerable to certain types of damage.