Why do you believe this? Remember the Shadowrun universe runs on some very different assumptions then our own. It's a lot more dystopian people do horde information as it's power, people often don't have time to code freeware as it is better spent finding food. In shadowrun literally if it's worth doing it's usually worth selling.
It doesn't actually have anything to do with the setting, though SR1 did come out before most people had heard of Free Software. It's just a somewhat clunky balance mechanic, because the original SR4 Matrix rules were built around the assumption that "programs are gear", and all gear has to cost money.
However, anyone playing a hacker wouldn't take long to start wondering why they can't get programs for free using their leet skills. There's several realistic ways to do it, be it pirating commercial programs, using free/open-source software, or (if the character is really good), writing their own software from scratch. It would seem unrealistic if these options didn't exist, but they ended up making PCs jump through a lot of silly hoops to go this way, to somehow "make up" for the fact that they wouldn't have to spend money.
If it was me, I'd probably have gone with a rule system where programs didn't matter at all, or didn't matter as much. That way, you could just assume hackers got them for free one way or the other.