At the end, when Rorschach decides to reveal Veidt's plan out to world, Manhattan gets in his way and Rorschach says:
Of course, you must protect Veidt's new utopia.
What did this line mean ?
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Here's the corresponding scene from the graphic novel:
Rorschach is mocking Dr. Manhattan, who is also a utilitarian like Veidt. Veidt cares little about single human lives in the greater picture, but Dr. Manhattan literally does not cares about single human lives in the greater picture, because he doesn't possess empathy. He's also hyper-logical, and recognizes that Veidt's plan has merit.
Rorschach, on the other hand, sees the world in black and white, evil vs. good, and Veidt's plan being morally grey is unacceptable to him. Here's their exchange immediately prior to the scene in question (it also shows up in the film), which shows both their viewpoints very well:
In the scene you speak of, Rorschach realizes that "of course" his and Dr. Manhattan's views on the matter are direct opposites, and that due to this it's inevitable that Manhattan must "protect" Veidt's plan from Rorschach – and that obviously, given the good Doctor's nature, he will succeed in this protection.
Of course, in the film, Dr. Manhattan dooms himself as well here (as Veidt framed him). He does not literally do so in the comic, where the nature of Veidt's plan is different, but it can be argued that he irrevocably dooms his own humanity (which has been deteriorating throughout the story) in the process.
So Rorschach not only realizes that Dr. Manhattan will act as a utilitarian with regards to the blood Veidt has spilled, but that he will act as a complete utilitarian, against his own personal interests and banish himself for the greater good.
Incidentally, since we're talking primarily about the movie, I thought the changes made to the ending in that adaptation made sense. Veidt cares about himself and his legacy, but he knows Dr. Manhattan shares his moral beliefs, doesn't care about his own legacy, and has the power to protect Veidt's plans.
Of course, you must protect Veidt's new utopia
Rorschach lives in a black and white world, and he cannot be part of Veidt's plot, no matter what the consequences
No, Not even in the face of armageddon Never compromise
He has however left a journal on its way to the 'New Frontiersman' saying 'whatever happens, it's a plot by Veidt'
Knowing he cannot stop Manhattan, he chooses to sacrifice himself to protect the document, and his statement is cajoling Manhattan to do the deed. Remember Nite Owl 2 has described him as a great tactician and highly unpredictable, and this is his strategy.
Allowing himself to be killed to keep Veidt's secret would be a compromise (and show him to be weak) , that's not the reason for his sacrifice.