I'm sure it was possible to punch the compiled executable as an option, but I was a student during most of my keypunching days so the cards would be read by a card reader the computer would compile the FORTRAN and then execute the program, reading input data from cards that were stacked behind the source code.

One summer, I worked at an engineering firm and had to run a program frequently on a set of input; it's possible that the executable I was loading into the card reader was already compiled and not the original FORTRAN source, but I don't remember for sure.