He didn't want to be credited.
From a Guardian article:
Moore has a complicated relationship with money. "Pure voodoo," he
says now. "Only there as long as we believe in it." Challenged, during
a television interview this year, about why he would sign away the
movie rights to a comic such as Watchmen if he didn't ever want it to
become a movie, Moore said he gave up the rights because he never
expected any adaptations to happen; he called it making money for old
rope. But then the films came out, and somewhere along the way Moore
developed such a distaste for what he saw on the screen, and the
revenue accrued from it, that he asked for his name to be taken off
the credits; then he started turning down production money. Moore gave
his share of the Watchmen fee to Dave Gibbons, the artist with whom he
conceived the series.
His Wikipedia page goes into surprisingly good detail on his views on this. The page includes a summary of an article on Comic Reporter, stating:
Moore has subsequently stated that he wishes his name to be removed
from all comic work that he does not own, including Watchmen and V for
Vendetta, much as unhappy film directors often choose to have their
names removed and be credited as "Alan Smithee". He also announced
that he would not allow his name to be used in any future film
adaptations of works he does not own, nor would he accept any money
from such adaptations.
So effectively, he just doesn't want to accept any finance from it as he's not happy with the film adaptions of his work.
To quote one final article (from Left Lion):
You’ve always refused to put your name to film adaptions of your work.
I know this is going to be hard to put a figure on, but how much money
do you think you’ve turned down, for taking a moral standpoint on
Well, they asked me if they could give me a huge amount of money to
bring out these Watchmen prequel comics – which they were going to do
anyway - and that was probably a couple of million dollars. I should
imagine with all of the films it would be another few million? In a
way it’s really empowering to do that.
You can’t buy that kind of empowerment. To just know that as far as
you are aware, you have not got a price; that there is not an amount
of money large enough to make you compromise even a tiny bit of
principle that, as it turned out, would make no practical difference
anyway. I’d advise everyone to do it, otherwise you’re going to end up
mastered by money and that’s not a thing you want ruling your life.
Money’s fine if it enables you to enjoy your life and to be useful to
other people. But as something that is a means to an end, no, it’s
It's also worth noting that both Paul Levitz, president and publisher of DC, and David Lloyd, the V for Vendetta illustrator, found it difficult to sympathise with him. From the NY Times:
Mr. Levitz said that such so-called reversion clauses routinely appear
in comic book contracts, and that DC has honored all of its
obligations to Mr. Moore. "I don't think Alan was dissatisfied at the
time," Mr. Levitz said. "I think he was dissatisfied several years
Mr. Lloyd, the illustrator of "V for Vendetta," also found it
difficult to sympathize with Mr. Moore's protests. When he and Mr.
Moore sold their film rights to the graphic novel, Mr. Lloyd said: "We
didn't do it innocently. Neither myself nor Alan thought we were
signing it over to a board of trustees who would look after it like it
was the Dead Sea Scrolls."