Actual costs are unknown to the general public. Stated costs are bullshit numbers that may or may not be in close proximity to the real thing, but there is no way for the general public to know. We can know gross receipts (easy enough to verify). The "double the production cost" calculation is useless as it is based on unverifiable numbers. Many costs are offset by sponsors/product placement, or budgeted in different departments for tax purposes. There are far too many examples of people attempting to get their fair share for work done on films with major gross receipts who've been shunted aside by the "the costs were so high there was no profit" gag that any speculation on this is rather wasted.
STiD was profitable enough for there to be a sequel. That is really all one needs to know (unless one needs to be privy to the inner financial workings of Paramount). And even if a studio flat out says a film was a financial disappointment (which I've not seen or heard about Trek in such a direct fashion), it does not mean the film was not profitable.