This makes me think that the filter is only applied to images in the PDF. The Quartz Filter method didn't work for me, even when I applied a custom filter with aggressive settings. I had a PDF of handwritten annotations on a book exported from Goodnotes. This is for anyone who is in the same boat as I was. A follow-up poster even posted AppleScript code and Automator recommendations to make compressing PDFs a snap! Check out for more on that. Also, some nice guy on Apple's Discussion boards put up a bunch of premade filters you can download that do the same thing.
It's remarkably easy to make your own filter by modeling it off Apple's filter. When you start ColorSync Utility, you'll see how Apple programmed their "Reduce File Size" quartz filter that you see in Preview. With this program, you can create you own quartz filters which allow to you compress PDFs as much as you see fit. In Leopard (perhaps Tiger or earlier, I'm don't recall), in your Utilities folder you'll find "ColorSync Utility".
With Quartz Filters, you can take total control of the compression process. This is from a review of PDFCompress on : Ahhh! Turns out that you can fine tune the quartz filter that Preview uses.
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