[Publius6961]

Why was a plane with hydraulic problems not stopped at the end of the runway?

Occam's Razor.
Probably because the problem hadn't manifested itself yet.
Otherwise the plane would have run off the end of the runway.

D'OH!

[r9etb]

Probably because the problem hadn't manifested itself yet. Otherwise the plane would have run off the end of the runway.

The article says they had known hydraulic problems while still in flight.

[Bob]

From the article:

The DC-9 had reported hydraulic problems in flight,...

The hydraulic problem had already manifested itself during the flight. Once the plane had landed, I'd have expected that the possibility of the problem recurring would have been considered.