If by "protected" you mean that PDF files have DRM, you can use DRM
removal software to strip the DRM. It costs about $30, and it helps to
know what kind of DRM it is.
If by "protected" you mean that the PDF is secured so that people can't
save or modify it, I haven't figured out how to deal with those files
either.
If you're referring to things like Google Books, you should be able to
read them with Adobe Digital Editions. The newer versions are
accessible. I haven't tried, but I know it's accessible because two
screen reader users have told me they use it. I'm assuming it's similar
to Adobe Reader.
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