It's not just about strengthening the muscles though. What about everything between your muscles.

Although I tend to agree with you in part... If you are a regular runner then you are probably doing enough during the runs themselves to strengthen your joints and ligaments, and some supplemental machine work is only going to benefit you.

Think you'll find if you go "arse to the ground" on your squats, you'll be bringing your hamstrings into play quite enough.

I can completely understand the need to target specific muscles, hence the need to use machines, and not everybody has the knees/mobility/balance to perform a correct squat.... But to a newcomer to strength work, I would always point them in the direction of working on light squats before pointing them towards the machines.

For the record my leg specific strength workout includes only squats and standing calf raises, although admittedly I do sometimes hit the machines for a quick blast. Although I come from a kickboxing background so I do already have a decent 'base' of strength in my legs.