It's no secret on here that Honeymoon in Vegas remains one of my favorite shows ever. It was a true treat that I still believe deserved a better audience. To your question, though, a few things:
1) Geographically speaking, the Nederlander Theatre doesn't help any show. I believe Honeymoon was initially supposed to go into the Atkinson on 47th, which would've been a wonderful spot. Unfortunately, being south of 42nd Street simply does not get foot traffic near your marquee.
2) The show opened in January, which was a truly horrible choice to make. Unless you're opening with Hamilton-level buzz, distancing your show 4+ months away from Tony nominations season doesn't help one bit, and you have to be prepared with super deep pockets to get through the dark winter months.
3) It didn't have the "name" that a Broadway show needs these days. From what I saw at least, Tony Danza's name in 2015 elicited a lot of "aww yeah, I love that guy"s, but not enough "aww yeah, I'll buy a ticket for that."
Those are, I think, three fundamental reasons that led to its closing. Another one might include the fact that it was a "fluffy" show during a season of otherwise "important" theatre (for me, though, that was a plus). But, as Brantley's Critic Pick will forever attest, it was a truly wonderful show that just wasn't produced in the right way at the right time.