I am learning that having a human rated Falcon 9 rocket is very difficult. Would it be better to have 2 versions of the Falcon 9 rocket? I figure a human-only version would be easier to design with human-safety first. Then a cargo-only version would be more reusable and economical. It seems more difficult to have one rocket version for both missions right?
In a sense SpaceX did just that: they started with a cargo-only rocket and gradually improved it with their two goals of reusability and human-rating in mind. This plan meant the rocket was already generating revenue while the human-rating was underway. And building the cargo-only version first gave the team valuable experience that now helps reduce the effort in designing the human-rated version.
If they'd start developing the human-rated version in 2008 in parallel with the cargo version, they would not have had the knowledge they do now. Development cost would be higher than it is now.
Your suggestion would also mean running two design efforts and two production lines in parallel. This duplicates effort (making the process take longer than it does now) and makes the logistics more difficult (more factory space needed, twice the inventory etc.).
A lot of the effort that goes into human-rating a rocket also helps reusability: more reliable components, larger structural margins all mean the chance of being able to reuse a rocket 100 times increases.
SpaceX's focus on reusability also means there is less pressure on making the rocket cheap to manufacture: the manufacturing cost will be spread over tens of launches.