Ann Coulter isn't transgender. The reason the clip is offensive is because it is calling a transwoman a man. It is transphobic and nothing can change that. As for Media Matters, it may be poor taste to use that song to put her down, but it is different. Cis women don't have people denying their identity saying they are men with a "cut off penis" It's the context of the joke; not simply the joke in itself.
Still, I think it's a weak point for Media Matters and don't approve of those methods. Besides there are ways to criticize Coulter without going to that level. Just read one of her books and pick out one of the many inaccuracies.
Having said all that, I find it interesting that people need to choose examples from both sides. I'm a left winger, but I don't need to defend those on my side. Wrong is wrong. Actions are more important than ideology or the person it comes from. Case in point is Anthony Weiner. There was a time when I respected him. Now, after all the lies, I'm tired of him and feel he can't be trusted. Sure I can try to justify his actions by pointing my finger at David Vitter and Mark Sanford, but that doesn't justify any of their acts. It's a debate tactic that is irrelevant.