The argument isn't that the companies are necessarily doing the wrong thing for shareholders, but that cheap money is not spurring investment in capital equipment, R&D, etc., which is a change from what historically happened. The opinion of some people quoted in the article (not all) is that this lack of investment is bad for the economy long-term.

I don't read this as a critique against the companies, but against the reliance on the fed's current mechanisms for impacting the economy.

It's of course contrary to what proponents of the tax cuts claimed would result from the cuts. If logical consistency is important for you then the discrepancy might matter to you but if not then there are probably some more policy proposals for you to consider.