There is currently quite busy discussion about modifications of config.bin (or its text equivalent config.cpp) in other topics of this forum. Let me explain why we implemented "config modified" message.
When modifying config.bin, you can control many aspects of the game, some very important (like reload times or other waepon, ammunition or vehicle parameters, some not that important, like weapon sounds or other "minor" things.
We considered a lot what parts of config should be protected against cheating, and after some thinking and experimentation we decided that modifing almost any field in config can be used to get some advantage.
Let me consider two favourite config.bin modification types that seem innocent: sound replacement packs and face set replacements.
Sound replacement packs
Most sound replacement packs currently available replace original ingame sounds by other sounds, that are considered more reallistic or simply nicer by its creator. Exactly the same technique can be used for cheating: consider replacing very quite H&K sound (or sound of footsteps of eastern soldiers) by some distinct and very loud tone. This would give you quite big advantage, as enemy would be unable to approach you unheaderd.
Face set replacements.
Most common face set replacements replace original faces with some cammo type / spec ops faces. The very same same technique could be used for cheating: imagine replacing all faces with bright yellow face. This would make spotting enemy much easier.
While the message about modified config does not necessary mean given player is cheating, it tells you is it is impossible to guarantee he is not, as identical techniques can be used for non-cheatig and cheating config modifications. When seeing this message, it is upon your decision if you will believe the player when he tells you he is not cheating.
If you are using some config modification that is causing this message, you should understand why some people / servers may be unwilling to play with you. They see you are using modified config and they cannot know if you modified it in cheating or non-cheating way. If they want to stay on the safe side, they will often kick you or even ban you from the server. Seeing the number of people that used config modification to cheat, you can hardly blame them.