Who is considering the Cubs an underdog any more? Many people are rooting for them, but very few think that they are still an underdog after the last two seasons they've had.
If we're talking who unaligned fanbases are rooting for, we're talking decisions based on emotion, associations to qualities that might be unfair, personal anecdotes, and history. Viewing them as the underdog can be a matter of context, not just 2016 run differentials.
Boone happened 2 days after Bartman and 1 day after the Cubs had a 5-3 lead in game 7 before Beckett came in in relief and slammed the door. I had sympathy for them before my own misery. Since then, the Cubs have gotten swept in two consecutive Division series, and then again in the NLCS the next time they reached the postseason - much like our own sweep-y futility in 1988, 1990, 1995, 1998, and then the ALCS in 1999. They were also the better regular-season team in a majority of their World Series appearances since 1908, including 1910, 1918, 1935 and 1945, plus the 1984 and 1989 NLCS.
They also went through the wilderness structurally, committing to 3 years of utter ML futility under Theo & Jed Hoyer in 2012-2014 before seeing it bear fruit last year and now this year. That's fairly admirable patience and planning in and of itself. Basically, if there's any franchise out there that deserves our sympathy (absent a personal reason for a rooting interest), it's probably the Cubs.
You want to hate them for Joe "super-genius" Maddon? Fine. You want to hate them because screw the NL, I always root for the AL in the WS and pitchers batting is stupid? Sure. You think Ricketts is a smarmy carpetbagging patrician? I won't say otherwise. But if you've got no strong opinion going in, I see plenty of reason to root for them to break their own streak of bad luck (slash bad management, slash shitty ownership, etc), and for their fanbase to have to ditch the sob story and become just another club.