The distribution terms for Bison-generated parsers permit using the parsers in nonfree programs. Before Bison version 2.2, these extra permissions applied only when Bison was generating LALR(1) parsers in C. And before Bison version 1.24, Bison-generated parsers could be used only in programs that were free software.
The other GNU programming tools, such as the GNU C compiler, have never had such a requirement. They could always be used for nonfree software. The reason Bison was different was not due to a special policy decision; it resulted from applying the usual General Public License to all of the Bison source code.
The main output of the Bison utility—the Bison parser implementation file—contains a verbatim copy of a sizable piece of Bison, which is the code for the parser's implementation. (The actions from your grammar are inserted into this implementation at one point, but most of the rest of the implementation is not changed.) When we applied the GPL terms to the skeleton code for the parser's implementation, the effect was to restrict the use of Bison output to free software.
We didn't change the terms because of sympathy for people who want to make software proprietary. Software should be free. But we concluded that limiting Bison's use to free software was doing little to encourage people to make other software free. So we decided to make the practical conditions for using Bison match the practical conditions for using the other GNU tools.
This exception applies when Bison is generating code for a parser. You can tell whether the exception applies to a Bison output file by inspecting the file for text beginning with “As a special exception...”. The text spells out the exact terms of the exception.