Yah, I agree with Line. I used to try to organize my weekly routine so that squats and other lower body exercises would follow my long run by 24 hours and precede my next run by 48 hours, but I've found it doesn't really matter that much. And now I'm trying to run almost every day so it's become impossible to separate the two anyway.
But I don't do really heavy squats. My max is my BW, 225lbs/100 kilos, which is quite a light ratio compared to serious lifters, and I often do less, more like 125-175 lbs. I also do my squats after deadlifts, (which are just 1.5 BW), and power cleans, so I'm good and warmed up.
Right now my (idealized) schedule is the following:
Sun: Run - Hill Repeats/Sprints or short recovery run or rest;
ST - Polymetrics & Mobility with ankle weights
Mon: Run - short recovery run or Hill Repeats/Sprints;
ST - Upper Body (Chest, Shoulders & Arms)
Tu: Run - 5-7 miles Tempo/Aerobic
Wed: Run - short recovery run;
ST - Lower Body (Deadlifts, Power Cleans, Squats, Good mornings, Leg extensions, Leg curls, etc.)
Th: Run - 5-7 miles Tempo/Aerobic
Fri: Run - short recovery run;
ST - Mid Body (Rows, Pull-downs, Hyperextensions, Pikes, t-bar swings, etc.)
Sat: Run - 7-12 miles long run
I don't believe the squat is dangerous per se, but it is an exercise I'm extremely cautious with, because, as Neil's experience shows, it's easy to screw up one's back and/or knees with really heavy weights and/or by not building up the weight very slowly. If you're doing squats to improve your running, and not for overall fitness, I would think hill repeats/sprints would get you better results. But I don't really know what I'm talking about. This is just my own self-perception.