Imagine this: You're at a symphony concert and the orchestra is about to play Beethoven's 5th symphony. As the music begins, you are immediately STUNNED by the intensity of the opening motif: dun-dun-dun duuuuuuuuun. The volume alone is enough to knock you backwards, and the rhythmic precision is unbelievable.
The extreme angst you feel that's being conveyed in just four notes, the sound of death knocking on the door. You're SO READY to hear the follow-up of the second dun-dun-dun-duuuuun... but suddenly...
Somebody in the audience coughs.
The moment is shattered. All intensity drains from the audience, who is suddenly brought back to ground-level. Oh yeah. This is just a piece of music we've heard a ton of times and it's just really popular and recognizable.
Why do people think it's okay?!
Any musician will tell you that the silences are JUST AS IMPORTANT as the notes. Silence means tension. When somebody coughs, scoots their chair, or whatever during silent moments, tension is completely shattered. Imagine you're watching a movie and just as the two main characters are about to confess their love, somebody in the theater coughs and you miss the whole thing. The tension of the moment is ruined.
I think people have the idea that it's okay to cough during silences because they aren't covering up the music. But is it worth breaking the tension in art that the composer and the performers have worked so hard to deliver?
Here's a better alternative for you: cough during the music. You have my permission. I would much rather somebody cough during the loud moments when fewer people will hear than somebody ruining the sanctity of silence.
You'll be bothering less people. More noise (coughing, a squeaking chair, heaven forbid a phone going off) during a loud moment is MUCH less disruptive. People are also quicker to forgive duirng loud moments.
The people around you recognize that you're a human and have to cough, and the people across the concert hall won't hear any of the sounds you make because the brass section is louder than their thoughts anyway.
The only time coughing during a silence would be acceptable is coughing between the movements. (Which, there are no silences between the movements of Beethoven 5, so you've got plenty of opportunity to cough during loud moments.) The tension has (mostly) resolved by the time the movement is done, so you're free to readjust in your seat and clear your throat and check your program or whatever.
If everyone could just have the same understanding that coughing during a loud moment is much more acceptable, everyone's concert experience would be a lot more enjoyable.