I think yes, but only if you're not a complete dick about it.
Consider the many many people over the years that have made free games, or art, or music.
Complaining about it in the sense of complaining about having seen it, is a little stupid.
But, if it's sort of, good, but not great (or even quite bad), it may be worthwhile to point out it's flaws anyway.
Assuming it isn't incredibly mean, the creator of it may well appreciate some honest feedback on their work.
After all, they do presumably care whether what they've created is any good or not, and if nobody is willing to say anything negative about it just because it's free, then they will basically never know what they are doing.
Is it good? Is it bad? In what way is it good or bad?
Something specific about it that's dragging it down?
Is it a good idea with a flawed execution? (technical problems, bugs, etc), or maybe it was just a bad idea in general?
How will they ever know a thing if nobody is willing to say anything?
If something is free, the nature of the complaints may have to be different. And arguably, you should be more lenient (especially say, with bug fixes and the like for a free game, because presumably the creator is using their spare time, and may have incredibly limited resources that make fixing certain technical things quite challenging)
The standards may be slightly different, but that doesn't mean you should hold off on any kind of criticism whatsoever.
As long as you aren't being mean about it, and are considerate of the limited resources they may have been working with compared to the kind of stuff you pay for, I think it's perfectly legitimate to voice any complaints or feedback you might have about something even if it's free.
(Of course, if it's free for another reason, such as a marketing stunt or something, that's slightly different again. Because while you might not be paying for it directly, someone was, so that subtly changes things again...)