The advertising clause is not a limitation on freedom. The 4-clause BSD license is a free software license; it just happens not to be compatible with the GPL (not all free software licenses are).
The reasons for this are very practical: not only does it place additional restrictions on the software (which is not permitted by the GPL), but if multiple 4-clause BSD projects are used, each project requires its own separate advertising statement (the 4-clause license does not permit combining these into a single sentence): https://www.gnu.org/philosophy/bsd.html
> The reason the GPL is annoying is that free license with an advertizing clause have existed for a very long time and are actually widely used.
Most modern projects using permissive licenses use 3-clause BSD, MIT/X11, or Apache, all of which are compatible with the GPL. In this day and age, choosing a 4-clause BSD license is a fairly conscious decision to make the project incompatible with the GPL.