The rationale is that enough effort is required to convert source code in printed form to a functioning product that it is not necessary to license programs in print form, at least at this time. I can attest to this based on my personal experience a few years ago when a student tried, and failed, to produce a working version of the Data Encryption Standard from the source code in Bruce Schneier's book Applied Cryptography. Scanners and humans are error-prone, so unless one understands the program, it can be difficult to find and remove the errors. Thus, in attempting to control only those artifacts that are easily used to encrypt, the government's distinction between electronic and printed materials is not irrational. I am concerned about the long-term implications of attempting to treat software generally as fully protected speech.
Software has the potential of being highly destructive.
Witness the Morris worm, computer viruses, or today's concerns about attacks on information infrastructure. Future viruses might someday bring down the power grid or direct the production of weapons of mass destruction. Yet treating software as fully protected speech could lead us down that path. Export control regulations express judgments that exporting certain technological artifacts are harmful to the national well being and that the regulations make an important difference. It is reasonable and legitimate to question whether these regulations are serving the country.