Viscosity isn't what matters. Sand and gravel do not harden when force is applied and will spread apart as I'm sure you can imagine.

They're already hard. They won't spread apart because they're in a hole.

The individual pieces may be hard, but the collection is not. Think about walking in the sand. Your feet sink down and the sand will flow up and over the sides of a container. Gravel is the same way albeit to a lesser degree because the pieces are larger.

With a sheer-thickening fluid, when sheer force is exerted on it, the entire collection of fluid affected by that force hardens in reaction so it would be like running over the top of a bag of hardened concrete.

You're assuming there's a large surface of it. There's a rigid container for the little bit of sand (the pothole). Filling it with gravel works very well (we do it a lot in Greece as a temporary measure). The problem is that the gravel gets thrown out of the hole bit by bit by cars, but the solution in the article isn't meant to be permanent either.

a liquid will return to a flat hole-filling shape if it's altered, gravel does not. Also not great to spread gravel around your road, especially if it's used by bicycles. Gravel also hinders repair work

I also like the idea that the bag could be coloured to assist cyclists in avoiding them..

Dirt roads? gravel roads? And the bag keeps it together. But I'm also not a civil engineer so I'll take your word for it.

The bag will rip and tear over time because the contents are shifting independently of each other. This will not happen (as quickly) with a non-Newtonian liquid. Not to mention, dirt and gravel roads aren't big bags. The materials are simply laid out on the ground. They also don't last very long under high traffic or heavy loads.