Debian packages often combine multiple projects into one package. The copyright file typically contains very accurate descriptions of which parts are available under what license. The copyright file will usually contain glob patterns that match specific files to some license.
The result is that yes, the libprotobuf-dev package in its entirety does contain GPL parts. This does not mean that the library in the package is subject to the GPL.
The copyright file explicitly declares its format, typically the format described at https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/. The file consists of paragraphs, each of which map files to a license (identifier or full text) or map a license identifier to the full license text. You should therefore read the file from the start, not from the end where there is just the full license text.
E.g. my version of the package (
3.0.0-9.1ubuntu1) contains the following paragraph:
2009 Dirk Eddelbuettel <firstname.lastname@example.org>
2016 Dmitry Smirnov <email@example.com>
2016 Laszlo Boszormenyi (GCS) <firstname.lastname@example.org>
2009 Julien Cristau <email@example.com>
2013-2014 Robert Edmonds <firstname.lastname@example.org>
2008,2009,2010 Iustin Pop <email@example.com>
The package source contains some GPL-covered files, but these are just used for the packaging. They don't affect the library at all. The source also contains an GPL with Autoconf Exception licensed file, but that doesn't affect any dependent code.
If you do not feel comfortable using a Debian package you can always download and build the library yourself. However, Debian packagers are very good at checking the actual licensing status of the software they package, rather than simply relying on the declared license of a library.