acquired a negative connotation.
[Edit: As pointed out in the comments, it has always had a negative connotation.]
If you tell or even insinuate to someone that what they are saying is a conspiracy theory you can be assured that the conversation will soon be coming to an end and the person might begin to dislike you.
Perhaps there is a conspiracy in this, but the word itself has become tainted with terrible imagery. When you hear "conspiracy" you start thinking of a bearded crackpot wearing a tinfoil hat living in a cabin the woods with no internet connection and a shotgun by the bed.
If you tell someone that you think what they are saying is a conspiracy theory they will start to think you are seeing them as the bearded crackpot. They might think you do not respect them (who respects that type of character?) which can lead to resentment and eventually dislike. This is fine if you are talking to someone you don't like, don't know or have no intention of becoming friends with. But when you are talking to friends and / or family members this is not the desired outcome. Even when you don't think this about your friend of family member they can still become offended.
So the question is, how can you tell someone that you think what they are saying is a conspiracy theory without offending them?