I was also highly irritated with the ending--although I watched the anime, instead of reading the manga, which I think was a mistake; Urasawa's genius at pacing and emotional manipulation doesn't carry over as well off the page.
That said, the ending felt like a cop-out.
MAJOR SPOILERS beyond this point, that will ruin your enjoyment of the series completely.
Seriously, don't read this if you don't want to know how things end, from the point of view of a vehemently upset reader.
Doctor Tenma spends years training and tracking the man whose life he saved, because he feels responsible for the actions that man has taken, and when he finally tracks down the titular monster, as a town is rent asunder around him...
...a hobo runs up and shoots Johan in the head so that Tenma can save his life again, reaffirming the naive idiocy that got him into this mess in the first place. Nothing was learned, except that 'violence is bad for you.'
Tenma never confronts the fact that he cannot be held responsible for the actions of patients he rescues, nor is he capable of acting directly to bring the greatest villain the world has ever known to justice. (Maybe shoot him in the leg, if you can't bring yourself to kill, still, after all the situations you've through were people were shooting at you when you had a gun in your hand?)
The fact that Johan disappears just makes this disaster of an ending even worse.