For the sake of argument, I'll ignore the evidence of them being made by humans for the moment.
So, ignoring the evidence for the moment, a question or two comes to mind for those who think that crop markings are made by aliens.
So...you've got aliens with technology so advanced that they can act physically on Earth. That means they're either here physically or can somehow act physically over vast distances. However they do it, the point for this question is that they can act physically on Earth with precision and for extended periods of time.
So why would they use that to make large, complex marks in fields? If they wanted to communicate, they could do so far more effectively. If they wanted to remain hidden, they wouldn't make large, complex marks in fields. The binary message one assumes that not only can they act physically on Earth, but they also understand binary, the ASCII standard and English and probably the way that optical discs work (since the pattern mimics an optical disc). If for some reason they thought that was the best way to communicate, why such a message? Why not "Greetings to the people of Earth from <whatever they call themselves>" and a message that means something? Why not instructions on how we can communicate with them? Even if that's with binary crop circles, they would at least tell us where to make them. "Leave a message in the field next to this one", or something.
The only answer I've seen to these question was comedy from Douglas Adams - it's all adolescent aliens, probably drunk, who are messing with primitive civilisations (i.e. us) for a laugh. While a joke, it's the only explanation I've heard that accounts for the the bizzare behaviour of these hypothetical aliens.