Sure it does and they should apply that exemption to everybody. We're all equal but now some are more equal than others.
Ask yourself this Luis. Is the corporation that runs the New York Times a 501(c) non profit? Of course not. So if I buy an ad to criticise Lieberman or Dodd within 60 days of an election by wiritng a company check, I go to jail. If the New York Times slimes conservatives every day of that 60 days, no problem because they are more equal than I am.
Of course some day they will target "hateful right wing media" and they will have to adjust the exemption but by then nobody will give a crap.
Peace bro.
If that is true, you are right that it is violating our freedom of speech. However, if it is true that you may buy that ad as long as you do it with hard $ and disclose the source of that $, then most of the outcry is baseless.