It's all a holdover from assembly-line factory jobs. You need to start at a specific time and work hard the whole shift. If you're 3 minutes late, the line is delayed by 3 minutes. Software development is a very different profession.
The problem, in my experience, is when they bring in non-technical managers in, preferably from completely other environments (production / manufacturing / industry).
Luckily it's getting more rare these days, but I've seen managers that were hired on the basis "a good manager is a good manager, no mater where he/she comes from", only to manage production floor like a factory.