The phrase "let's agree to disagree" often occurs in everyday conversations as a way of communicating the notion that the discussion has reached an impasse; a point where the two debaters have proposed two incommensurable ideas that no amount of further discussion could overcome. But often, especially in discussions on science between opponents and detractors, this phrase is used in an attempt to conflate opinion with fact and philosopher Michael Stokes has written a good article on the topic: "No, you're not entitled to your opinion". He starts the entry with a speech he gives to his first year philosophy students:
“I’m sure you’ve heard the expression ‘everyone is entitled to their opinion.’ Perhaps you’ve even said it yourself, maybe to head off an argument or bring one to a close. Well, as soon as you walk into this room, it’s no longer true. You are not entitled to your opinion. You are only entitled to what you can argue for.”Stokes goes on to highlight the relevance of Plato's distinction between "opinion" (or common belief) and "knowledge" to this popular equivocation, with the former expressing uncertain claims and the latter representing claims which are certain. For example, subjective beliefs like, "Red is a prettier colour than blue!" or "Nirvana are way better than the Foo Fighters!" are uncertain and are essentially just a matter of taste or preference. They are not claims which could really be proved one way or the other. However, claims like, "All unmarried men are bachelors" and "There are no square circles" are certain and are not claims that can be reasonably questioned or attributed to subjective preference.
Anyone who has argued with people on "controversial" topics, like evolution, climate change, vaccinations causing autism, etc, will recognise this tactic where presenting the scientific consensus of a position is dismissed as being just "your opinion" and demand that you accept their opinion as equally valid. This is, more or less, the entire basis of the creationists' argument behind the "Teach the Controversy" movement.
What this all means is that when people try to tell you that, for example, the fact of evolution is just your "opinion", or they try to weasel out of a discussion by suggesting that you should just "agree to disagree" as if the subject you're debating is something that you simply choose to 'agree' with, then don't be fooled into accepting it on the basis of misplaced etiquette and politeness. Scientific conclusions are not claims about the world that we have tastes or preferences for; we don't choose to accept that 'vaccinations work' in the same way we accept that blue is pretty. We accept scientific conclusions based on the evidential basis for these positions and the evidence either supports it or it doesn't, and so if someone wants to "disagree" then make sure that they understand that it is not a matter of opinion. Disagreement either suggests knowledge of evidence which refutes the scientific conclusion or it represents a rejection of reality itself.