Anime can be truly confusing to those that aren't really schooled in what anime is all about. Even then, there are some anime features that even long-time fans can get thrown off track by. While there are plenty of anime series' out there that are easy to understand, there are others that might throw the viewer for a loop.
This is one of the reasons why anime has trouble really getting into our culture, moreso than just a niche placement. It's this barrier of understanding that blocks the path to true success. Some of it has to do with cultural differences, while other aspects come in through critical thinking and the way the story is fed to the viewer.
Are audiences outside of Japan just unwilling to actually think about a series when watching it? Are we expecting a show to tell us exactly what's going on and what the motivations are, in no uncertain terms? Is that the case, or are some anime features just too deep into their country of origin's culture that the localization result doesn't make for good viewing?