You could take out a city's communications systems without killing anyone or destroying any buildings. In addition to the obvious benefits for the inhabitants, this also avoids the sort of bad press back home that can fuel opposition to a war. But that doesn't make these weapons totally safe, especially if they're being used to mess up the electronics of aircraft. This means that you can set off your weapon and inflict damage without having to get close to your target. According to some estimates, a flux compressor detonated at an altitude of few hundred metres could wipe out electronics over a 500-metre radius.
Electromagnetic weapons can be sneaky, too.
You don't have to fry everything in sight. There's no shrapnel, no burning wreckage, no smoking gun. The downside is that it can sometimes be hard to tell when an electromagnetic weapon has done its job. This is compounded by the fact that unless you know exactly what kind of electronics you are attacking, and how well protected they are, it's hard to know how much damage a weapon will do. This unpredictability has been a major problem for the military as it tries to develop these weapons.