When the libertarians use such a flag, they risk sending out the signal that they are dogmatic in their thinking, full of hatred for all non-libertarians (which means vast majority of the population), and alienated from the society. Your philosophical, economic, and political thinking might be good, but few people will come forward to support your cause if your calling card contains the image of a rattlesnake with its fang bared and the text “DON'T TREAD ON ME”. People have a poor sense of history—most of them may not even know about the connection with the Gadsden flag.
Some libertarian scholars, I have noticed, use the image of a hemp leaf as their flag. Perhaps they think that that the hemp leaf stands for liberty and good life. I believe that people should be free to consume the intoxicants of their choice, but to use a hemp leaf as the flag for a social and political movement is not a good strategy as it creates the impression that this is a movement of the hedonists, by the hedonists, and for the hedonists.
The “DON'T TREAD ON ME” flag and the hemp leaf flag should be rejected because they create the impression that the libertarians are a community of unhinged and alienated people. A social and political movement is also about winning—your flag should be such that it helps you in making a positive impression on maximum number of people.