I have found that when I actually apply my critical knowledge skills - questioning the status of procedures, rules and arguments- I pay a price.
It may be that I am ignored or I am excluded. Or judged difficult. But the point is that even when we do enable our students to be users of knowledge - and encourage them to question, the pressure within society - our institutions - effects a price.
The price is usually economic and social exclusion.
Hmmm..What to do then?
I have three major pieces of advice, gleaned from years of hard experience of exactly what you describe here.
1. Pick your battles
2. Find your friends
3. Show results
The first means applying a judicious hand. My experience has been that most discussion in meetings, committees, etc., is unreasonable and illogical. People make decisions based on poor evidence, bad reasoning, bias and prejudice, and worse. It's ongoing and you can't stop it.
And, as you pointed out, these same people will react badly when you attempt to inject a note of reason into the debate. Your considered and fact-based reasoning will be interpreted as a personal attack. No matter what pains you take (and you should!) to depersonalize the matter, to make the subject of debate and not the person the locus of discussion, people will think it reflects badly on them if you disagree with them.
So, pick your battles. Let the small stuff go. A lot of what matters will not have any long term impact. Don't enter into arguments you can't win. Identify what is core for you, what you can't or won't back down on, and raise these issues consistently. You still won't be successful when you raise your points. But your consistently will serve notice to other people that on these points they need to be much more careful before leaping in.
The second applies to picking your friends. It's really hard to be the lone voice of reason at meetings or in committees, and often, you don't have to be. Be observant and watch for people who apply reason and evidence to their considerations. Make it clear to them that by arguing in this way you will respect their position and potentially modify your position accordingly.
These are people you can work with, and people you should gravitate toward. If your current venue of activity contains no candidates, find alternative venues. Some venues (like, say, staff meetings) cannot be avoided, but if they are unproductive, invest your energy and commitment elsewhere - to subcommittees, special interest groups, professional associations - wherever you can find voices of reason.
You can also find friends by being clear about how you reach opinions, and by (in the parlance of fifth-grade mathematics) showing your work. This will identify you as a person who gives thought and consideration to logic and evidence, and hence identifies you to others as someone who can be worked with.
Finally, third, produce. As someone (Dan Rehak? Wayne Hodgins?) once said to me, "quality ships." It is all very well to have opinions, however well-versed, but the best evidence that you know things, can work through evidence, and evaluate priorities, is by "shipping", or actually delivering results.
Do the work. Write the background papers, do the interviews with clients, draft the policies, write the software, design the deliverable - whatever it is that your group or association does. In my work here at NRC the strongest argument I have for my opinions is that I deliver results. Disagreeing with me or blocking my work has a cost to the organization.
But also, by doing the work, you are providing tangible assistance to the people you are currently disagreeing with. You are providing a set of accomplishments they can hang their hats on, through their association with you. There's an old saying for public speakers, "love your audience," which really works, because if you are focused on how much you want to help and support your audience, you lose all your self-consciousness about speaking in public. It works in the office as well.
The person whose voice is most respected in any group is not the person who leads, or is smartest, or is even right. It is the person perceived by the rest to have the least self-interest, the person who is there to help rather than the person who is there to pursue an agenda or toot their own horn. A minute spent helping the other person achieve their ends (which are often not even in conflict with yours) is far more productive than a minute spent arguing with them.
I hope this helps.