Couple things at work. First, I think all the people who appreciate Harper and were just kinda bummed about how it all went down and want to get past it stayed home for a depressing, cold, early April rain-delayed game (this describes me- you would have had to pay me to go last night), while the people who wanted to boo him bought tickets. That was probably the biggest factor. Another factor is the obnoxious Philly fans who travel south and act like complete dooshbags when their team is good and then vanish when they aren't. I generally think Philly sports fans get an undeserved bad rap- I've have been to Phillies and Flyers games in Philly and had a great time, met some awesome people. But the fans who bus down to Nats Park suuuuuuuuck, and Harper signing with the Phils brought them back. So that didn't put anyone in a pleasant mood. Also, Harper has not handled the departure very well. Nats fans are usually very welcoming of former players- Wilson Ramos and Ian Desmond still get cheered, Blake Treinen got a big ovation at the ASG last year even though he sucked as our closer to the point the Nats had to trade him for Doolittle, and there's other examples. So it's not like we're predisposed to resentment.
Also, regarding the contract- remember you're only getting the Harper/Boras side of the story in those reports. It's in their interest to make it seem like Harper got severely lowballed and had no choice but to move on. For example, they haven't explained why they never reached out to the Nats to negotiate a better deal. All they had to do is pick up a phone and call, but it appears they never did.
Anyway he still didn't deserve that, and it sucks, and it made Nats fans look bad, and now Trea is out for months and a banged-up 1-3 team is about to go on the road to lose a bunch more games to the Phils and Mets and everything is terrible. At least the Wizards fired Ernie Grunfeld.