Anytime a film version of a popular book diverges from its beloved source material, it's the alterations themselves that cause the most backlash. When Zack Snyder's Watchmen, an adaptation of Alan Moore's classic graphic novel, arrived in theaters to a reception that ranged from lukewarm to infuriated, one may have assumed that same conventional wisdom was the explanation. Instead, the opposite was true, more often than not.
Much of the fury graphic novel fans leveled at the movie version of Watchmen had to do with elements Snyder transposed directly from the panels to the screen. There are things that work in comic books, and there are things that work in movies, but not many that work in both. The director's overzealous loyalty to the source material was often the very problem.
Of course, there were plenty of instances in which the movie departed from the book (the absence of a giant squid, most notably), and those choices brought their own problems, sometimes drastically altering the story's message. Then again, a movie like Watchmen can be something of a Rorschach test in its own right, with reactions deviating one way or another based on familiarity with the original text, or lack thereof.
Dr. Manhattan (Billy Crudup) is not viewed as a villain at the end of the comic book; in the movie, he is. That's a significant departure. Let's ignore for a moment that the giant squid - which in the original pages of Watchmen targets New York, courtesy of Adrian Veidt/Ozymandias (Matthew Goode) himself - is nowhere to be found in the film version. Making Dr. Manhattan the bogeyman may ultimately unite the world against a common enemy, but in the movie, the common enemy becomes the vigilantes/superheroes/what have you, instead of a giant squid. So, the question at that point becomes what will the lives of the main characters in the story look like going forward? Probably not good, but there's no way to know. What's more, this ending paints the governments involved as innocent bystanders rather than the ones truly at fault for a world in chaos.
This is a pretty big sticking point. In the comic, Dr. Manhattan is the only character with powers. While there's no suggestion that the other characters in the movie version have actual powers, so to speak, they're simply too capable as heroes and crimefighters. On the page, Nite Owl II (Patrick Wilson) is a clumsy brawler, almost too inept at fighting to really justify being a vigilante. In the movie, his inexplicably enhanced skill set is exemplified when he and Silk Spectre II (Malin Åkerman) take on an entire squad in an alley, easily dispatching them and having fun doing it. Similarly, Rorschach (Jackie Earle Haley) kicks a ton of butt. The fighting is too slick, the fighters too gifted. These people are not superheroes - that's kind of the whole point - yet Snyder too often depicts them as such.
Adrian Veidt felt he only had one way to save humanity, and that was to drop a giant squid on New York, wiping out thousands to save more. It wasn't something he relished; it was an extremely painful choice he struggled to make, and it haunted him. In the movie, Veidt delivers an eminently recognizable bad guy speech at the end and actually says his nuclear strike on millions of people is "the world's punishment" for getting so close to WWIII. Conversely, in the comic, he insists: "I'm not a republic serial villain. Do you really think I'd explain my master-stroke if there remained the slightest chance of you affecting its outcome?" His character almost does a complete 180 in the movie.
The Comedian (Jeffrey Dean Morgan) and the original Silk Spectre (Carla Gugino) have a very problematic relationship, but not all of it was non-consensual. In fact, Laurie, AKA Silk Spectre II, is the result of consensual love-making between the Comedian and Silk Spectre I. When Laurie confronts him in the comic book, rightfully angry that he assaulted her mother, the Comedian is at a loss for words, unable to respond, unable to tell her the truth.
This moment in the book is complex; it's an opportunity for the Comedian to find some level of redemption (at which he fails), but it's also a moment in which Laurie comes close to discovering her existence wasn't as ugly as she believed. Ultimately, she doesn't discover that, so the story overall isn't changed, but Laurie's tragedy isn't well-developed in the movie as a result of the scene's absence. If nothing else, it could have given Laurie a bit of catharsis.