Gaiman has a certain tone that carries from his comics to his books to his screenplays. It's kinda obvious to say that his tone is dark, since that's what he's known for, but it's different from most darkly written things in that it has heart. This is definitely obvious in this book, which I would certainly hope, seeing as it was written for a juvenile audience.
It is, however, a bit offputting to be confronted by 3 deaths and one pending death within the first two pages of the book. I wonder how many countries/states have banned this book from their libraries and schools, even with its Newbery Medal in 2009. (Although I'm told that a lot of the most excellent children's books have deaths in them.) The gruesome nature of the deaths, even though there is no blood or gore or anything of the sort, was pretty darn disturbing. But, if you can get past that and into the next chapter, there's a good reason to stick with it.
It's the care Gaiman takes in constructing his characters that makes his setting more cosy than creepy. A young (live) boy living in a graveyard with the denizens (dead) of the graves could be decidedly creepy. Instead it warms the cockles of your hearts, watching the boy navigate among ghouls, slithery snake-y creatures, and really bad men. Gaiman does this best in the chapter about the Danse Macabre, changing the meaning and intent of the original legend, and leaving you with a warm, fuzzy feeling that...
Well, just read it, okay?