I don't think there's any one answer to that question myself -- the reasons are as diverse as the individual readers. Sometimes the author undergoes an ideological or philosophical transformation between books (or even just becomes bolder about expressing the views they already had) which leads to a irreconcilable conflict of my thinking and theirs, or pushes my tolerance for those differences over the limit. (See: Philip Pullman.) Sometimes it turns out that the things I loved best about the author's first book -- the style, the tone, the atmosphere -- don't carry over into subsequent novels because they were a feature of that story, not the author's writing as a whole (such as Beagle's The Last Unicorn, which I mentioned in the comments of Sherwood's post). And sometimes I eagerly expect certain things from a series or sequel to a book I really loved, only to find that the author had a completely different plan and veers off in a direction that doesn't interest me at all (I've heard several readers say this about Maria Snyder's Study books, for instance).
Then there's the rarer phenomenon when you love an author's prose but not their poetry (or essays, or what-have-you); or you think them brilliant scriptwriters (or lyricists) but terrible novelists, or the other way around. The ability to put together words in an arrangement that pleases you in one medium doesn't always carry over to others, and that can cause this kind of dissonance as well.
What about you? If you have a much-loved book or books by a certain author but found that most or all of their other works left you cold, what were your reasons for feeling that way? Feel free to comment on either my post or sartorias's as it pleases you; I'll see it in either case.