Hi,
Just adding in my 2 cents worth here, take it for whatyou can.
I have heard a number of different reasons for the classical lunge punch being trained so much, some seem to have some merit, others less so, and have basically come up with my own interpretation. The first thing to take into account is what I heard Charles Daniel once refer to as "the human element", that is, the when, where, and who of the situation. In our modern world, the classical lunge punch is not something we would commonly come up against (in this regard, I am refering to a stepping straight punch, typically aimed at the face); with the advent of the globalisation of media, most fighting systems have adopted similar approaches and aspects (leading to the MMA phenomena), and that includes the almost universal adoption of Western Hands (boxing). As a result, the more common hand strikes in a modern assault are jabs, crosses, and hooks from a balanced posture (for a skilled opponent), and wild swinging hooks, either stepping or standing solid (haymakers - less skilled or unskilled opponent). Almost all strikes are with the fists, and most are aimed to the head.
To contrast this, the classical Ninjutsu lunge punch is performed by starting with your punching hand as your rear; you then step forward, and punch in a straight line to you rintended target (there is obviously a bit more to it than this, but that is a matter for your instructor to teach). Ideally, this punch should also be retracted at the end, something that is sometimes "forgotten" to aid in a technique....
So why the different attacks? And why train against a punch which is so different than the ones you will most likely face? Well, the answer to the first part can simply be "the human element". THe second we'll get to in a moment.
By the "human element", I am refering to all aspects that influence the movements of an art. These include the style of clothing worn (armour, street clothes, the styles of the day), the type of conflict engaged in (battlefield, match fight/duel, rules, number of opponents, weapons etc), and various social conditioning beliefs (for example, in the West, kicking someone in the groin is frowned upon as "dirty fighting", but it seems to turn up quite readily in Eastern systems). With current assaults, there are a few different types, duel-type fights, and ambush assaults. In both, though, similar physical attacks are used, the difference is in the tactics used to employ them. Suffice to say the techniques are fast and powerful. They are based on Western hands, because they are also fast and powerful, and are designed to be used in either plain modern clothes, or even with your garments shed. They also follow the social rules of no kicking, or at least no kicking to the groin (we are, however, seeing a change in the style of assault thanks to the advent of things such as youtube and MMA. Ground fighting has become accepted, and group ambush assaults are becoming more common as gangs film themselves to brag online).
The lunge punch, on the other hand, follows the conventions of fuedal Japan. In the fuedal battlefield, you would be wearing armour, which would limit your movement. So in order to generate as much power as you can, the technique was developed to step with the punch, in order to get your entire bodyweight behind the strike (Ken Tai Ichi Jo - the weapon/fist and the body as one). This action also mimiced the movements used with a variety of weapons, such as sword and naginata.
The main reasons to continue to train it, and against it, are therefore not immediately practical. But neither is Muto Dori (unarmed sword defences). Nor spear techniques, or indeed most of the classical skills we study. So why train them at all? Most RBSD and MMA guys will probably tell you you shouldn't... but I feel that would mean missing out on some very important, time-tested skill building patterns, as well as meaning the loss of very rich, very beautiful old knowledge.
So in conclusion, your reasons for training the old techniques will be your own. You may train them to practice proper body mechanics which will carry through to the rest of your training, you might train them to gain an insight into a different culture in a different time and place, you may gain an appreciation for historical warriors, or you may just find it fun. Whichever your reasons are, realise that they may change as you grow more experienced, and your own understanding of the movements of your chosen art deepens.