Let's take a look at some statistics, shall we?
2010 Best Musical Nominees:
American Idiot
Fela!
Memphis
Million Dollar Quartet
Three of the nominees were some sort of jukebox musicals, two of which had more ambition (American Idiot and Fela!), and Memphis was the only original musical that season.
The older Tony voters felt American Idiot just wasn't their personal cup of tea, Fela! had been struggling at the box office (pretty much because a lot of people never even heard of Fela Kuti), Memphis was the little show that could, and Million Dollar Quartet's nomination was clearly the award.
2011 Best Musical Nominees:
The Book of Mormon
Catch Me If You Can
The Scottsboro Boys
Sister Act
Two of the nominees were crowd-pleasing musicals based on popular films (Catch Me If You Can and Sister Act), The Scottsboro Boys was a critically-acclaimed Kander & Ebb show that moved from Off-Broadway to Broadway, and The Book of Mormon was an original musical by the creators of South Park.
Mormon was clearly the juggernaut, Scottsboro Boys would've done better if it was still running, and the nominations for Catch Me If You Can and Sister Act was pretty much their awards.
2012 Best Musical Nominees:
Leap of Faith
Newsies
Nice Work If You Can Get It
Once
Three of the nominees were based on more obscure movies, two of which actually had a chance of winning (Newsies and Once), Newsies was Disney's first well-received musical since The Lion King, and Once was the more inventive show that moved from Off-Broadway to Broadway.
Leap of Faith's nomination was pretty much a win for not being Ghost nor Spider-Man, Nice Work If You Can Get It was just happy to join in, Newsies was already commercially viable enough, Once needed the Tony more.
2013 Best Musical Nominees:
Bring It On: The Musical
A Christmas Story: the Musical
Kinky Boots
Matilda
Two of the nominees were closed shows based on popular films (Bring It On and A Christmas Story), Kinky Boots was based on a more obscure British independent film, Matilda was a British-import based on a beloved Roald Dahl novel.
Kinky Boots kind of did seem commercially viable because of Cyndi Lauper's name, but the backlash against Matilda was that so many theatre producers felt screwed by The Royal Shakespeare Company for turning down their valuable offers to bring the show to Broadway, so several of those screwed producers got their revenge by voting for Kinky Boots.
2014 Best Musical Nominees:
After Midnight
Aladdin
Beautiful: The Carole King Musical
A Gentleman's Guide to Love & Murder
The most diverse group of nominees we've had in years. A revue, a big Disney musical, a jukebox/biography musical, and an operetta based on some obscure novel which also served as source material for an old Alec Guinness film.
After Midnight wasn't really a musical at all, Aladdin was Disney's biggest hit since The Lion King, some felt Beautiful could've won because it was clearly the more commercially viable, but voters felt Gentleman's Guide (the little show that could) needed the Tony more.