What are jinja for? This is a question that members of Jinja Honchō’s Oversight Council have raised recently, and that has been addressed in editorials in Jinja Shinpō, but I do not think that there is an official answer. Here are some of the options that seem to be popular in the Shinto world — they could all be true at the same time.
Jinja are places to venerate the kami. This is the most purely religious answer, and probably the closest to the original purpose of jinja. However, it relies on a belief in kami as something that would appreciate, or at least notice, veneration. This sort of belief is not universal among priests, and not even a majority view among people who do visit jinja.
Jinja are focal points for the local community. This is another popular answer with priests, particularly in rural areas. In some places, it seems to be actually true, but there are a lot of priests lamenting the fact that many people are losing their connection to their local jinja. It does not help if you move around a lot, because that means that you keep having to make connections with new jinja, and in urban areas with a lot of new arrivals, this function can be quite limited. Even then, of course, priests might feel that their jinja should serve this purpose.
Jinja are institutions that preserve traditional Japanese culture. This purpose is rarely stated explicitly, but it is implicit in many of the calls to preserve matsuri and traditional local kagura. This certainly appears to be true, but it raises a lot of questions about what “traditional Japanese culture” means — after all, a lot of the current rituals performed at most jinja were finalised in the early twentieth century under Western influence. There are, of course, also parts of traditional Japanese culture that are not really associated with jinja.
Jinja remind the people of Japan of the central role of the Tennō, and honour him. This purpose gets bound up with a lot of right-wing conservative nationalism, including issues of constitutional revision and territorial disputes. This does not, to most westerners, seem to have anything to do with Shinto, but in the official statements from the Shinto establishment it is rather more prominent than the idea that jinja are places to venerate the kami. (This may well be because everyone takes that for granted, and feels that they do not need to say it.)
The emphasis at any individual jinja depends on what the priests and ujiko at that jinja feel is important. I don’t really have a sense of the relative importance of these purposes across Japan, but I do get the impression that purposes other than these are not so important. It should also be obvious that these are quite different, and can lead to different decisions about what to do in certain situations. For example, if a jinja is primarily a location where the kami are to be venerated, then it does not, strictly speaking, need to have a local community. It might even be possible to preserve the traditional culture while no-one lives nearby, although that would be hard. But it is impossible for a jinja to serve as a focal point for the local community if there is no local community.
This also makes it difficult for Jinja Honchō to agree on anything simple and clear as the purpose of jinja — the diversity of Shinto goes all the way through, at the most fundamental level.