That article is full of logical fallacies and factual errors from beginning to end. But, I'll just pick out a few.
The main presumption is that if Libertarians had stayed in the party they were in, they would have a greater influence. But ask a traditional democrat, for instance, what influence he feels he has on his party. The likely answer is absolutely none. The democratic party has moved so far to the left that traditional democrats are feeling party-less, even if they still vote a democratic ticket.
Or ask a republican who believes in strong border security what influence he thinks he has on the party. Our border is still very porous. And, besides a few bones thrown to appease them, the official position has been, "Trust us about our border security policy, that it is right for you, even if you disagree with it."
In other words, the parties feel the need to dictate policy to their members, not to have policy dictated to them.
And I have actually watched Libertarian conventions on C-SPAN. I find myself in stark disagreement with the author of the article.
Plus, in my mind a wasted vote is a vote for a candidate that you don't agree with. And I don't disagree with the majority of Republican candidates mildly. I disagree very strongly.
It reminds me of that one Simpson's Halloween episode, where the two major party candidates are revealed to be two space aliens. Someone in the audience states that they'll vote third party. One of the aliens responds, "Sure, throw your vote away." At the end, when the human race is enslaved by the aliens, Homer says, "Don't blame me, I voted for Kodos (the alien who didn't get elected)"
You may not agree with my perception of the situation, but surely if it were a choice between two space aliens, you would not vote for one of them just to avoid throwing your vote away? I know that you like many (not all) of the Republican candidates. I don't. Are you saying that, even though I am convinced that it's a vote between a great evil and a greater evil, that I should still vote for one of them?

I heard a blip in passing this morning on Fox and Friends that there may be more to the two party hegamony (is that the correct word in the context?) staying in control than everything outside of their platforms just being "fringe".  It could deal with sheer economics of the election, which kind of coincides with something said in the article shiz linked.

Experts are estimating it is going to cost $1MM for the 2008 election for gaining control of the Whitehouse, between the primary and general elections.  So, based on that, for a candidate to even be considered viable, they have to have like (forgot what figure was given exactly) something like $250 million in their war chest just to not be considered a wannabe candidate in the primary.  And for the real rich people and interests, this is not a hard thing for them to provide the funding for the person they want in office.  They joked that for Obama then, all he needed to do was go on Oprah Winfrey and get her to endorse him and back him, as they felt she was worth like several billion dollars. 

But, the conversation reminded me that non-orthodox candidates and parties have little chance of succeeding simply due to the scale of political economics.  They have to get so much money and support before they are eligible for federal funding $, and yet even then, they will still get blown out of the water by the $ raised and matched by the big two parties' candidates.  And, until a party can muster enough clout to win the presidency, it is not going to be attracting a lot of people as a viable option.  Sure, it is an option, but there are only a few people who are comfortable with never being on the winning side when it comes to politics and election results.  Did what I say make any sense, or was I being too obtuse? 

In addition, the author of the article does not accurately represent the chances of a third party. He says that right now they have no chance of winning the presidency (probably pretty accurate), and that since they have no chance to win the presidency people will not vote for them in local races. This is ignoring reality, though. The number of 3rd party candidates in local positions has increased in recent times, despite the chances of a third party candidate for president not getting appreciably better.
Besides, third parties have in the past become viable. It hasn't really happened since Roosevelt's unsuccessful attempt to get the Bull Moose party off the ground. The Republican party wasn't always a majority party. It started in 1820. It's a specious claim that the way the Constitution is set up prevents a third party from ever getting off the ground, because historically it's happened.
The current political environment may make it very difficult. But if it's the right thing to do, then it should be done regardless of whether it's hard or not.
It all gets back to what Roper said: vote your conscience. If your conscience says vote for a Republican candidate, then that's what you should do. But my conscience says vote for candidates that support the principles in the Constitution party platform.