Of course you may use Powerpoint, but there are some decent reasons not to. First and foremost, Powerpoint simply isn't that good for drawing graphics (in my humble opinion), especially if you are doing diagrams like flowcharts. Visio is designed for this sort of thing as is the open source Dia. With diagramming software, the lines that link blocks stay linked to their assigned nodes which makes editing and adjusting the position of blocks easy.
If you do use Powerpoint, you need to make sure you are avoiding many of the features it provides (often by default) like color, drop shadows, 3D text, etc. You want a plain black line on white background illustration.