The arguement, generally speaking, is that if we create a two-tiered system, with one tier that circumvents the Geneva convention, other nations and powers would do the same. (They already do, of course, but they'd have our precedent to call it legal).
That means that if we had some guys operating out of uniform, and they got caught, it would be considered appropriate to torture them, since our own rules would allow it. (That's a largely symbolic distinction, since our enemies have never historically shied from torturing our POWs.)
Isn't that a slap at soldiers who do wear the uniform? Why would anyone sacrifice and volunteer to serve if they are disrespected by putting terrorists in civilian clothes on the same level of honor?????????
Here's how this problem began:
The Geneva conventions do not protect any armed force that operates without uniforms. The "uniform" can be as simple as a bandana or a shirt of a standard color, nothing fancy. It just has to be known and used. The rule was made to protect civilians, who would, of course, but unmarked.
It's not lawful to fight without a uniform marking, and it's completely lawful to execute someone on the spot for doing so. We simply choose not to. That means there's no disadvantage, and many advantages, for al-Qa'ida to dress as civilians.
We disregard a law meant to protect civilians by not executing the al-Qa'ida we catch. We have no one to blame but ourselves for that, and for the other legal troubles that stem from it.