Like it or not Fed, nadal and djoker are all still bigger draws than Andy, that's fact whether we like it or not. Organisers do what's best for ticket sales. I am sure Andy doesn't care one bit what court he is on, he will have his mind set on the match and the court won't cross his mind. Think how world number 4 Ferrer feels out on court 4....
The flaw in your argument is that tickets are purchased before anyone knows who is playing where. Popularity of the players, imagined or otherwise, isn't why people buy the tickets, unless of course you happen to be a Fed or Nadal fan, who give the impression that they would buy tickets for a pig pen if they thought their 'God' would turn up and hit a ball in it.
Personally I wouldn't put Djokovic on the main court today. The match with Goffin, frankly, is fairly unlikely to be a match (watch Goffin pull off the upset now!) so what's the point in that being on the main court?
It won't make any difference to Andy, but I think the organisers have got it wrong.