Charles Xavier's band of mutants, the Uncanny X-Men, have been an integral aspect of Marvel Comics since the title's start in 1963. The X-Men were Marvel Comics' marquee book as well as cartoon series in the 1990s, but the superhero team of outcasts were largely excluded from one of Marvel's biggest event series' Civil War by Mark Millar (Kick Ass, Wanted) and Steve McNiven (Old Man Logan, Guardians of the Galaxy).
The X-Men lacking integral roles in the main Civil War story-line of clashing superhero ideals, beyond cameo appearances, is owed to two prior Marvel events, namely 2001's E is for Extinction and 2005's House of M. The kickoff to Grant Morrison's landmark New X-Men comic run, E is for Extinction, saw Charles Xavier's villainous twin sister Cassandra Nova attack the mutant island nation of Genosha with a cavalcade of Sentinels, resulting in the estimated deaths of 16 million mutants. Four years later, the House of M story arc saw the mutant sorceress and former Avengers member Wanda Maximoff a.k.a. Scarlet Witch essentially render most of mutant-kind powerless with her vast abilities. In the aftermath of House of M, the Sentinel O.N.E. (Office of National Emergency) Program would be launched by deputy director Valerie Cooper and James Rhodes a.k.a. War Machine to protect the last remaining mutants located on Earth. At the start of Civil War, the mutant population is down to only a few hundred, which the X-Men are still attempting to come to terms with when the event kicks off.
Though they are fellow superheroes and occasionally operate in the same backyard, the X-Men and Avengers haven't always had the best relationship. Earth's children of the atom frequently save the world from hostile mutants or supervillains on a daily basis, before the tide re-shifts and the X-Men along with the entirety of mutant-kind are once again seen as public enemy number one. The X-Men have been fighting their own registration act for years and where are "Earth's Mightiest Heroes" The Avengers to be found? Another memorable Marvel Comics crossover event Secret Wars, from the early 1980s, saw the two superhero teams initially butting heads over this exact concern.
The X-Men were never major team players who found themselves involved in the affairs of other superheroes, the Fantastic Four or Avengers were much more persistent in that area. Instead, it's Civil War pro government registration figurehead Tony Stark a.k.a. Iron Man who attempts to recruit the X-Men to his side, but is instead rebuffed by telepath Emma Frost for largely turning his back on the genocide of Genosha. Though the X-Men decline Stark's offer, the group takes a neutral stance, preferring not to get involved in the coming war. Iron Man and Captain America having the full might of the X-Men team on one of their respective pro / anti registration superhuman teams would tip the scales in the opposing heroes' favor quite a bit.
Civil War is essentially a culmination of decades worth of storytelling throughout Marvel Comics. The X-Men have been hunted, distrusted, and wrongfully accused for generations, while Civil War finally places the larger Marvel population in the shoes of the mutants.