dragonprawn,
That's really a pretty poor analogy and I think you may already know that.

First, the drill instructor has only a very limited time to take people with absolutely no training or experience and make them marginally functional for a very specific and, for the most part, a very limited context. He has an artificially short time frame in which to produce results of any kind at all, so the training is weighted toward that particular limitation.
Second, the training he provides is designed with no particular concern for what is actually optimal for any individual soldier. That may be callous for some to learn, but that's the fact of the situation. The military has to provide that training which will take the most number of people, on average, and prepare them reasonably well within a very short time period. The trainers know full well that the training will be somewhat to grossly insufficient for a certain number of trainees, but it's a cattle drive and they're fully aware of that fact.
Third, the trainees are in the unusual circumstance that they are having to act in as much harmony as possible with a large number of fellow soldiers. Individually determined action is catastrophically chaotic with that many people involved. Soldiers must also follow a fairly rigid chain of command in order to for the army as a whole to act effectively and in order to protect as many friendly lives as possible. Even questioning orders, nevermind openly challenging them, can introduce a degree of chaos that is terminally destructive under many of the circumstances that an army faces compared to the individually-focused circumstances of the individual civilian martial artist simply trying to defend himself and perhaps a family member or two.
In contrast, individual civilian martial artists are not forced to act as part of a collective, and are therefore free to pursue training that is optimized to them as individuals in order to maximize the resulting self-defense capability. Unlike an army, at the scale of the individual, there is no such thing as degrees of acceptable losses, so the trainee is free to pursue training which maximizes his ability to protect himself and his charges.
The individual civilian martial artist is also not under the artifice of an unusually and sometimes unworkably brief time constraint during which all the training must occur before facing the very highest stakes for performance failure. While not a liscense to goof off, the individual civilian martial artist has the comparatively unheard of luxury of significant amounts of time available for training, sometimes even many years, compared to his typical military counterpart's 8 to 12 weeks, depending on branch of service. He is also thus capable of pursuing a depth of training that the average soldier simply won't be given opportunity to pursue, at least during wartime duty.
Further, even with all of these dramatic differences between the soldier dealing with a boot camp drill instructor and a civilian pursuing long-term development of self-defense skills explicitly outlined, it's still going to be true that the soldier, at least during non-combat duty, is free to question every single thing the drill instructor taught him with regard to individual hand-to-hand combat once he's moved on from boot camp. Many soldiers do exactly that and pursue martial arts study while still in active duty service. For example, you can rest assured that soldiers accepted into and actively participating in special operations duty have long since questioned, openly challenged, and even improved upon most of what they were taught as basic H2H in basic training from their drill instructor. It's all a matter of timing.
The drawing of an equivalency between the raw boot camp soldier in basic training and the civilian martial artist pursuing self-defense is ultimately nearly untenable. Even so, eventually even soldiers can find opportunity to question what they are taught in basic, and many even receive further training which occasionally even openly contradicts that prior training. As I stated previously, sometimes the learner must wait for the answer to his question and must be satisfied with saying, "I just don't know yet" until the answer is eventually made available. For the soldier in boot camp, that is just such a time. He must, for the time being, accept what he is given and work it diligently merely to stay alive in a wartime environment. Later, once he has the luxury of time in a non-combat environment, his circumstances begin to allow him to pursue the answers to questions he may have had to put on hold out of necessity.