I think what Gengis is refering to, is for example that more and more airfields tend to favour the use of one main runway,
for various reasons, noise abatement or licensing.
If you operate a Taildragger or Microlight which prefers grass and is more cross wind sensative than the usual crop of trainers that operate there, it sometimes has to be pointed out to ATC that yes they do have a grass runway and yes we'd be a lot happier using it please.
Integrating with the rest of the traffic is vitally important but not to the point of endangering yourself and your aircraft by accepting an instruction which puts you in a less favourable position than is otherwise available.
Most of the time the wishes of both Pilot and ATC will coincide however it is sensible if you believe that following instructions will endager you or others to query same.