Stealth Rock and Rain are the biggest reasons, with SR always being the bane of Fire Types and Rain becoming so prevalent this generation. And you forgot about Volcarona, who is OU.
The biggest problems Darmanitan faces this generation are survivability due to being entry hazard weak and the massive recoil off Flare Blitz, and the frequency of rain, which totally nerfs the primary reason to use it. Basically, it requires a lot of team support, and even with all the support in the world its only going to be sticking around for a few turns thanks to Flare Blitz and its less than ideal defenses. Finally, while it does have good speed it just isn't enough when there are so many key Pokemon that are able to outspeed it that can threaten it.
The bottom line is that Darmanitan just can't stick around long enough, and can't get its job done reliably enough to be consistantly OU. Add the fact that there are more versatile Fire Types available like Infernape and Heatran, and it's just not the first choice for most teams.