It's better than being unemployed, but may still "count against" people in the future. (Note that this does not mean I agree with such assessments, and also note that there is a difference between a startup and hand-to-mouth freelancing.)
EDIT: The second paragraph previously just said "It's better than being unemployed, but not all that much." Replaced with the above.
I think one of the great things about programming is that there is always a way to make a living. Can always start a startup or freelance.
But that is not what this article is about. Most the entrepreneurs they are talking about are not startup founders in the sense you mean. They are not trying to build the next big thing. They are instead working as individual contractors at poor pay (compared to what they had before at least) soley because they cannot get full time work.
While I do not necessarily think this should be held against them, especially not with the way the global economy has been lately, this is still a very different situation than being a startup founder trying to build something brand new.