There's some bug.
Here is code I use;
//Instantiate a Presentation object that represents a PPT file
Presentation pres = new Presentation();
//....do some work here.....
//Setting Write protection Password
pres.ProtectionManager.SetWriteProtection("test");
//Save your presentation to a file
pres.Save("demoWriteProtected.ppt", Aspose.Slides.Export.SaveFormat.Ppt);
In this case, the file does not protected.
If I choose pptx file format, everything works fine.