This show has always had two nominations on lock (lead actress, choreography). The choreography is pretty well done, mostly fun and interesting. I'm agnostic on it winning but it very well could. Joaquina Kalukango was incredible. She has tough competition in Clarke and she may not take it this year, but she has multiple tony winner written all over her if given the opportunity. Lighting was also excellent and unsurprising.
Otherwise it's competing against a relatively weak field for those 4th/5th technical spots and a lot of them aren't surprising. Costumes and set were fine. Even score, which sounds ridiculous for it to have received at first, it only beat out Diana and Doubtfire. The one that is egregious is book. The book was bad.
Other than book, Supporting Actor is the slot that is most surprising. Clayborn Elder, Jefferson Mays, Chris Fitzgerald, maybe David Paymer, Shuler Hensley, Christopher Sieber, most of whom already have nominations or awards and are in better shows, well, they all probably thought if they lost out on a nomination it would be to another of them. I'm very surprised by both nominations. What DuPont and Shivley have going for them is probably their strength in the strong choreo. They do pull it off. Was Sydney's dancing better than Fitzgerald's comedy? I mean, no, but I'm not the most upset about it. Company men have not historically gotten featured Tony noms (1 across the last 3 productions, although with the gender swap it gets a little muddled). Critically, MM has not done much better than PS, although I would probably go Sydney/Mays if I was picking two from those two.
After all of that, a musical nomination just follows. The people who took Sydney over Clayborn Elder clearly liked PS more than those other shows in that last slot. I'd imagine if there were only 5 nominations in the category that PS misses out.
To answer your original question, what you seem to be missing is seeing the show. It's poor reviews are unsurprising and largely deserved, but where PS shines it shines bright, and it was just lucky that there was a lot of weak this year.
Let It Burn will be the best performance at the Tony's.