Most importantly, in the quest for safety, convenience for non-car traffic is almost always sacrificed, making car travel all the more enticing. This is the wrong feedback loop to have.
Semi-recent example. Problem: number of accidents involving people crossing the street too high. Solution: remove zebra crossings. Now don't get me wrong -- this has reduced street crossing accidents. But it has also made foot travel much more inconvenient, because you now have to either walk much longer to find a crossing, or wait for all traffic to pass and then make a mad dash for it. (As a side effect, car travel got a bit more convenient because there are now fewer places you're expected to stop.)
This repeats in all shapes and styles constantly. In the name of safety, cyclists are re-routed for almost a mile (!) around what was previously a hundred-yard straight line.
The underlying problem, I think, is that planners see that car people are trying to get somewhere. They don't seem to realise that pedestrians, cyclists, etc are also just trying to goddamn get somewhere. These activities are almost universally treated as a hobby or pastime. (You see this even on the local Craigslist-type sites, where bicycles are not under the "vehicle" category where I would expect them, but under "hobby".)