If you're not averse to using the terminal, there's a package called qpdf that you can install. It's in the software center. To remove protections from your file you can use something like this:

qpdf --password=your_password --decrypt yourfile.pdf output.pdf

That should do the job. As a side note, another useful (also command line) tool to have for working with pdf files is pdftk.

Example from man pdftk:

pdftk secured.pdf input_pw foopass output unsecured.pdf

Hope that helps!