Here are some excerpts from Azar Nafisi's introduction to a new edition of the novel (published, and slightly edited, on The Guardian's website, 5/13/2006) that may indicate why it was banned by the Iranian government. In brief, it criticized the state of society and government in Iran at the time, and also talked about "love and eroticism" in a way that many puritanical Muslims might object to.
The very structure of the novel, its use of farce, and its frank and
entertaining investigation of love and eroticism go against any
fundamentalist or puritanical doctrine, be it Islamic or otherwise.
[...]
Although the book is not political, it is politically subversive,
targeting a certain mentality and attitude.
Pezeshkzad's Dear Uncle Napoleon can only exercise his petty tyrannies
within his own household, yet he also represents far grimmer dictators
with much greater power to harm.
Sometimes it seemed to me when I still lived in Iran that My Uncle
Napoleon predicted and articulated in farcical terms the mindset
ruling over the Islamic Republic. Like all totalitarian systems, the
Iranian government feeds and grows on paranoia. To justify its rule
the regime had to replace reality with its own mythologies. The
Islamic regime based its absurd justice on Uncle Napoleonic logic,
destroying the lives of millions of Iranians through its laws, jailing
and torturing and killing all imagined enemies and accusing them of
being agents of the Great Satan, namely America and its allies. If
Uncle Napoleon felt that the delay in his nephew's train was a British
plot, the guardians of morality in Iran saw a woman's lipstick or a
man's tie as props/accessories in an imperialist plot to destroy
Islam.
[...]
To lie is a way of life, and it is justified because telling the truth
has unpleasant and sometimes fatal consequences. Thus a community is
created based on illusions and fantasies.
[...]
Although My Uncle Napoleon is highly critical of the society it
depicts, it is also the best testament to the complexity, vitality,
and flexibility of Iranian culture and society.
This review from The Seattle Times (Valerie Ryan, 5/5/2006) calls Napoleon's garden a "microcosm of the larger world." The Iranian government would probably not be delighted to hear themselves described as regularly "trembling with rage."
I was not able to find any list of banned books in Iran on the first page of Google results that included My Uncle Napoleon (1, 2, 3, 4, 5, 6).
Wikipedia, citing the "1988 Act of the Guidelines to Publish Books, by the Supreme Council of Cultural Revolution of Islamic Republic of Iran," lists several reasons why a book may be banned. The reasons cited above may fall under one or more of those reasons, specifically "mocking and weakening the national pride and nationalistic spirit," "renouncing the fundamentals of religion," and/or "creating an atmosphere of losing national values to the culture and civilization of western or eastern colonizing systems."
Renouncing the fundamentals of religion; promoting corruption;
inviting the society to riot against Iran; promoting the ideas of
terrorist and illegal groups and corrupted sects and defending
monarchy; stimulating conflicts between the various ethnic or
religious groups or creating problems in the unity of the society and
the country; mocking and weakening the national pride and
nationalistic spirit, and creating an atmosphere of losing national
values to the culture and civilization of western or eastern
colonizing systems.
For more information on the reasons for book censorship in Iran, see these Wikipedia articles and "Criteria for banned books in Iran."*
*Note: that article mentions, and links to, a list of 200 banned books that was given to a bookseller. That link is dead, and the Wayback Machine does not have a useful capture of that page.