Current viruses are only spread by running an infected program on your machine. The Virus then installs itself in your System file (as well as some other places) and from there, infects other applications. The System file contains programs that run in the background, behind all other programs, handling low-level actions like accessing files and putting up dialog boxes. When a program like MacWrite wants a dialog box put up, it asks the System to do it, simply supplying information such as what to put in the box. Since the system runs behind all applications, it is the ideal place from which to infect other programs.
