For example, we have freedom of speech, but we can't yell "fire" in a theater. As well, the Supreme Court ruled in 2008 in District of Columbia v. Heller that while the Second Amendment grants individuals the right to own firearms, it does not extend to all firearms.
Were the amendments in the Bill of Rights meant to allow us to yell "fire" in a theater, to threaten the president, to own the biggest cannons of the day, etc.? Thank you.
A very, very common misconception of the first amendment is what you said, that you cannot yell "fire" in a crowded building. The reason that is not allowed is because it is not speech. It is a call to action. This is how it was explained to me, with an extreme example. A white person could walk into inner Detroit and yell "I am a racist! I believe black people are sub human and white people are inherently better than black people because of their skin color." That (as horrible as it is) would be protected by the 1st amendment, as it is a person speaking their mind regardless of their situation. Conversely, the same person could not walk into a Black Lives Matter meeting and lie "The guy in a red shirt and cargo pants said all black people are sub human" and have people go assault the guy in red. That person is not responsible for free speech, they are responsible for a call to action. It is likely that they did not intend for such calls to action to be protected
Rights can be limited. Indeed, it is theoretically possible for amendments to be completely repealed (the 18th is a real world example of that happening). Theoretically even the Bill of Rights are subject to being repealed (although it is extremely unlikely).