Look for a sturdy handle, too! I wanted a metal handle with metal finishings and fasteners. The handle and corners of a flute case take the most abuse, so I always liked corner covers, too.
I've seen the soft-sided flute cases, but I never felt comfortable using one. I always preferred a hard sided case with thick padding and a velvet lining. I always felt the hard sided cases didn't allow the flute to react as much to temperature changes, with the heavy padding and the velvet. Maybe that's just my imagination, though.
I guess the sling handles on the soft-sided bags make them easier for students to carry when they also have books and so forth, but I just like the extra security of a hard sided case.