Sorry, I don't know of any such tools, other than a one-off thing I wrote to help myself convert Doxygen's XML output to protobufs. I've attached that code to this e-mail. It is completely undocumented and it has parts that are specific to the Doxygen format that I was working with, so it probably won't help much except to give a vague idea of how this would be done.
The .xsl file contains XSLT code to convert an .xsd to a .proto file. The .cc file is a corresponding program which converts an individual XML document to a protocol message, given the .proto file produced by converting the XSD.