Trump actually tweeted as much in 2015 when the redskin name controversy was going on. He said the president should focus on more important things than the NFL.
I see the issues as very different. The Redskins name issue was just the WashPost and some lefties trying to whip up controversy where there was none. It died when the Post ran a poll and discovered that 90% of actual Native Americans, as opposed to SJWs, didn't have a problem with the name.
The flag controversy is a bit different, as it involves a highly politicized group of wealthy blacks who imagine themselves role models virtue signaling to a captive audience. That would normally be a matter for the league and ownership to address, but they have failed miserably and allowed the National Anthem ceremony to be exploited in a way that most Americans find highly offensive. Particularly since the NFL has made a show of wrapping itself in the flag and supporting the military(of course they charged them for that privilege), it is appropriate for national leaders to criticize the lack of respect being shown the flag and Anthem.