Well, advertising will indeed always be a problem for news organizations. But they need to get their revenue from somewhere, and with subscription revenue basically a thing of a past which is a damn shame, by the way) the primary source of revenue is now advertising.
The difference, I guess, is rather subjective. Normal advertising, say for a car company or toilet paper, is acceptable on the grounds that people are used to bull

in such advertising. Now, granted, we may be "used" to bull in political advertisements as well, but (and yes, I am showing some bias here myself) they tend to be much more subversive in nature. There's also the problem that political advertising is aiming for a direct effect upon the nation's political systems and policies. It's much more powerful and subversive -- and dangerous.
There is also a basic journalistic code of conduct that places special emphasis on having an objective viewpoint towards politics; people who fail to do this are considered to be bad journalists to one degree or another. It's a tradition born from the problems of Yellow Journalism, among other things; a little investigation into that particular snake's pit will give you a good idea why news organizations (should) shy away from any potential political bias.
@Caius: it's true that nobody ever tells the whole truth; the idea is to try your best, hence the problem of political advertisements.
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