One of the best things about the scientific method is that it offers a well-defined metric for telling the difference between good ideas and bad ideas; since the whole purpose of science is to create a (naturalistic) theoretical framework by which to describe the real world, it therefore follows that ideas that are not supported by direct observation of the real world are bad ones. Thus, in science, when an ideology goes head-to-head against established fact, the ideology should lose every time.
The scientific method is, of course, based in the goals of science, and is not universally applicable to every domain of thought* but the same principle applies universally to any field which makes substantive statements about the real world. Theories can be beautiful things; they can be eloquent, powerful, internally consistent, and easily explained. But if they say something about the real world which simply isn’t true, then you need to go back to the drawing board. It’s harsh, but it’s the way that it has to be. An example I might cite off the top of my head would be the Bohr model of the atom; sure it’s pretty; it’s even useful in certain contexts (just as it’s useful to talk about “sunrise” and “sunset” even though the Earth is the thing which is moving**) but it doesn’t work so you have to get rid of it.
Unfortunately, certain people don’t view theories as tools; they view them as pets, or even children. They love their theories; they try to keep their beautiful babies well-fed by shoehorning all observations, no matter how tangential, into supporting it. And they are protective of their theories, as a parent is protective of their child. Which means that any nasty facts which show up and try to destroy their theories must be beaten down.
An obvious example of this in action would be fundamentalist religion, which by definition, adherents must accept unquestioningly. Thus if the Bible tells you that the universe is 6,000 years old, the universe is 6,000 years old; all contradictory information is wrong. Thus do I, as a physicist, get occasional e-mails from crackpots who dismiss all of the astronomy of the last five hundred years because it disagrees with the literal interpretation of a single line in the Koran***.
Secular ideologues can fall prey to this as well****; maybe it’s just me, but I’ve noticed strong tendancies this way amongst libertarians and Marxists (for whom Dickensian working conditions and Stalinist Russia, respectively, are really just consequences of their ideas not being fully implemented). The present government of Canada is a particularly terrible offender; not only does it suppress evidence which opposes its ideology (and punish anyone who speaks out), but it has moved to pre-emptively undermine the chances that opposing evidence will ever be brought to light in the future.
I honestly think that this tendancy is one of the great underrated motivators of intellectual history; bad ideas are kept around for ages after being discredited just because someone is in love with them.
*Something about which many scientists need to be reminded on occasion
**Actually that’s a bit arbitrary, as you can define the reference frame which ever way you please, but my point is that geocentric terminology is still useful if you’re not describing things in detail.)
***”And He is the one who created the night, daylight, sun and the moon, all swimming in an orbit,” (The Prophets:33). The crackpot in question claimed that this proved that planets move in wavy orbits rather than elliptical ones (because of course it’s impossible to swim in an elliptical pattern).
****I hate to keep beating this particular drum, but I used to think that this was the reason that Radical Feminists hated transsexual women; now I’m pretty sure it’s something much more vulgar.