Reb,
RAW is not a standard format. It's not really a format at all. RAW just means "it's in the manufacturer's unprocessed format, with info about the pixel data." As such, every manufacturer's RAW format is currently different. So a software provider can't say "We support RAW," but rather "We support RAW formats from cameras X, Y, and Z." And it has to be specific cameras, too -- Canon's RAW format for their D60 camera is different to that in their 1D mark II camera, etc.
So to say that "Nominally the Fuji has the same RAW image format" as your D50 is not correct at all -- it's like saying English and Swahili are both languages, and because people speak languages, they should be able to communicate. Not so easy 😟
For now, my best advice is, if you want to use Aperture, make sure you're using a camera that is explicitly listed on Apple's pages as having RAW support. You can always send feedback to Apple via their Aperture pages.