I go for a 5km before work 2-3 times a week, with a longer run at weekends. I was doing crunches and other weight based exercises on the off days, but have been advised to do it after my runs.
My question is, why is this a better way to do it?
If you do them on the same day, your body has at least one full day of recovery between workouts. Running is largely a cardiovascular exercise once you're in good enough shape to do it effectively (which at 5K I would consider you to be). Effectively, it will get everything loosened up, warmed up, and slightly tired for you to have an extremely effective workout. So, you'll build more strength and tone (or bulk if you work it that way) by doing your other lifting and exercising immediately following your run.
Having a complete day of rest (or 2) in between workouts enables the body to more effectively and completely repair itself, meaning you'll be working everything again from it's peak, and not keeping your body and muscles stressed all the time. Currently, your routine works almost your entire body every day, and that's literally just too much; your body never gets a rest.