Yep, that's exactly right mate, with you on this. Rooney is a national icon, the biggest name in the league, he's our greatest, most recognizable current player, and the biggest commercial attraction, he's been at United since he was 18, he's the biggest power broker in the dressing room, he's on the verse of breaking the club's all time goal-scoring record so there will be a huge sympathetic backlash, etc etc. Even if all those factors wren't at play, in a vacuum, Van Gaal being a pragmatic man is not going to mess with a good situation (in terms of where the team is heading) entering just his second season at the club, and risk what he's trying to build.
The collective weight of the media will immediately be on Van Gaal's back (they don't even like him that much to begin with), and the magnifying glass will be solely on the Van Gaal-Rooney narrative, so there's a massive chance of things blowing escalating if the results don't match up once he's dropped. He can handle the criticism somewhat, but we really don't need that distraction at this moment in time to hinder the team's chemistry and development. Summertime, when there's no club football being played, we can ride the storm a bit, especially with the whole EURO focus. Rather do what Mourinho did with Lampard, than what Brendan did with Gerrard and deal with the fallout in-season.
Also, a bit more context to the Van Gaal dropping captains like Van Bommel, or falling out with players like Riquelme and Toni argument - there's a consistent theme will almost all of them without exception. eg. Van Bommel had been at Bayern for just 3 seasons prior to Van Gaal's appointment, and he was Dutch. He might have been the formal captain, but the most influential players were Schweinsteiger and Lahm, those two were the real heart of the team. Stripping Van Bommell off his captaincy was analogous to moving Van Persie on. Great contributor to the club, but at the end of the day he was an outsider despite landing the 20th, his time was up, and he had to go. Minimal fuss in the media, goodbye Robin. Wayne Rooney, meanwhile, is a totally different proposition. For his and the team's sake I hope he improves soon.