Is anyone really surprised? I think not.
I think that, to some extent, Cat's Cradle lives in the shadow of Vonnegut's Slaughterhouse-Five. The latter is undeniably a great book—in my opinion, the best anti-war book of the twentieth century—but Cat's Cradle is, to my mind, more incisive, less overtly cynical, and less blunt than its better-known and more widely read brother.
The story is fairly simple (begin spoilers): an everyman narrator named John (or Jonah, as his parents "nearly" called him) is working on a book about the bombing of Japan during World War II. In so doing, he ends up interviewing the children of Dr. Felix Hoenikker, a physicist who helped create the bomb. This results in his discovering a strange blue-white form of ice invented by Hoenikker and hoarded by his children, ice-nine, which turns any water it touches into a variant of normal ice that remains solid at room temperature; an extended visit to the fictional Caribbean island of San Lorenzo and its dictator, "Papa" Monzano; the discovery of its "suppressed" religion, Bokononism, and its eponymous founder; and, by way of ice-nine accidentally falling into the ocean off the coast of San Lorenzo, the end of the world. (end spoilers)
If you've ever read Vonnegut, you know one thing about him: he was simultaneously deeply cynical about the state and future of the human race and deeply hopeful that it would someday overcome its considerable shortcomings. Cat's Cradle illustrates this beautifully, juxtaposing the simplicity and near-Zen quality of Bokononism against the dictatorship of "Papa" Monzano and the backdrop of the horrific destruction wrought by humanity in World War II. At the same time, Bokononism itself (and Bokonon in particular) display the same struggle between cynicism and hope, producing such aphorisms as "The hand that stocks the drug stores rules the world."
Why is this book banned/frequently challenged? Well, there are some Bad Words in it. And one chapter (number 36, "Meow") featuring a message written in human excrement and a dead cat with a sign around its neck sporting the chapter's title. Certainly the relentless and overt probing of religion in general and Christianity in particular don't endear the book to school districts in the Bible Belt, and I imagine there are some school administrators and parents who are afraid exposing their children to Vonnegut's multilayered cynicisms and criticisms will turn them into nihilists or Satanists or something. The fact that they're missing Vonnegut's subtle but unmistakable hurt for the human race makes their desire to censor it all the more ironic.
That said, you won't find a more eloquent or compact criticism of humanity (particularly America) anywhere, especially not one tempered by Vonnegut's earnest love for the world. I'll say he's in a better place now, and not because he's dead or in heaven or anything like that, but simply because I think he'd find that funny. To Vonnegut, nothing was more serious than a joke, and it's when you aren't clear whether Vonnegut/John is kidding that you are, I think, at the very heart of Cat's Cradle.
I'll leave you with this, the last lines of the book and the last attributed to the enigmatic Bokonon:
If I were a younger man, I would write a history of human stupidity; and I would climb to the top of Mount McCabe and lie down on my back with my history for a pillow; and I would take from the ground some of the blue-white poison that makes statues of men; and I would make a statue of myself, lying on my back, grinning horribly, and thumbing my nose at You Know Who.
It doesn't get any better than that.