Pat, actually your misunderstanding is at the unix level and has nothing to do with perl. Stdin is a totally different concept from command line arguments. The two are somewhat related by the standard use of filter programs which can be called like this:

filter_program FILE1 FILE2
generate_data | filter_program
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The first form will read its input from the named files; the second form (with no command line arguments) will read its input from stdin. Both forms write their filtered output to stdout.