Actually, that's one of the few things that make sense in this book.
Daisy's training means she's only above average in the game she's in. She's facing foes with superior training, firepower and experience. Nick Fury is the only buffer between her and a slow and painful death. And he's being a complete douche.
Nothing else about this series makes sense, though. How Hydra has been running Shield for decades, why Fury is relying on a bunch of wet behind the ears kids or how these kids are supposed to be from off the grid sources. Fury found them by asking social services!
IMO, there's no evidence that the writer has thought his plots through. And IMO, spy stories may not need airtight plots, they need to at least stand up to inspection. And Secret Warriors don't.