Reason links to http://www.associatedcontent.com/article/1867049/libertarianisms_worst_enemy_is_not.html?cat=75 on why the biggest threat to libertarianism isn't big government; it's big business.
I've said it here before and I'll say it again: being pro-business does not equal being pro-market. Sadly, the business world contains more James Taggarts -- who want to use government to rack up political profits -- than it has passionately pro-market Dagny Taggarts. But as I also said in that post, all too many young libertarians don't understand that point clearly.
I don't know exactly why the fallacy persists, but I suspect it's at heart a structure of social change problem. See also. That is, most of the libertarians whom I've met who work at Level 1 of the structure of social change (the universities) or Level 2 (think tanks) are completely clear on this point. It's younger libertarians and pro-market conservatives, usually interns who are newer to the professional libertarian community, who get most tangled up on this point. So I suspect something's getting jammed in the transmission of libertarian ideas from the think tank world to larger audiences. That happens; it's an inevitable weakness of social change enacted along the model.
I'm tempted especially to blame Atlas Shrugged, which is of course one of the most popular introductions to libertarian thought out there. I don't mean to hate on Rand. It's an excellent novel. But it does deliberately romanticize big business, and so it perpetuates the unfortunate stereotype that all free market types are just shills for large business.