At the BFI screening I went to, we were provided with the interpretation of a New Jersey teenager called Margaret Stackhouse, written shortly after the film was first released (and available online here). Stanley Kubrick fully endorsed her reading, so it's likely the best place to look if one is searching for a guide to the film's ambiguities. Although Stackhouse builds alternative explanations into her analysis, the transcendent nature of the monolith (the mysterious object driving the plot of the film) is inescapable. Like the god Prometheus, it is there at the "Dawn of Mankind" to give us the tools to improve and murder each other: the forbidden fruit from the Tree of Knowledge. And at the end, a rapture. Stackhouse allows for either a capricious or a life-sustaining God, but it's some sort of interventionist God alright. In this regard it is worth comparing 2001 to last year's Gravity, in many ways just as visually impressive and innovative (and far more propulsive in a narrative sense) but also fundamentally concerned with the incredible unlikelihood that we have managed to get even this far. Gravity's commitment to our loneliness in the universe makes it the more coherent and admirable film.
It's telling that Kubrick's preferred analysis comes from a 15-year-old. No slight on Stackhouse intended, but there is something adolescent about 2001 in its complete devotion to cosmic musings at the expense of character. In fact, the only moment of human connection comes at the beginning, where space scientist Floyd has a skype conversation with his daughter, whose birthday he will miss. Interestingly, Kubrick used his own daughter Vivian for the scene, and that one slice of (autobiographical?) family life outshines an awful lot of the ponderous mechanics and dizzying lightshows that follow.