Well, now you're contradicting yourself:
So, was it, or was it not clear at the beginning that it was supposed to be an alternate universe?
Let's be clear about what the films show though. The beginning of the film in ST09 is the point where Nero intrudes and, to borrow Doc Brown's language, skews off into an alternate Trek universe. Although this isn't necessarily made immediately clear by the film, this ambiguity is in service to the story.
The film does make it abundantly clear that it is an alternate universe. They use it in dialogue. Young Spock has that line about "whatever our lives might have been....."
That's not peeing on your leg and telling you it's raining, that's bashing you over the head with "THIS IS AN ALTERNATE UNIVERSE!!!!!"