Other checks on the tyranny of the majority, like protecting the rights of individuals (in light of shared values) in the face of a majority decision to violate them is hard to characterize as tyranny at all.
Requiring legislation to pass two bodies with different weights is an interesting move which isn't precisely the former; it deserves a weakened version of the same criticism, and it is not entirely clear whether it pays dividends to make up for it. I agree with the implied premise that decisions are more likely to be good ones if they look good from more angles.
There is much ink spilled in apologia of the current system around how the needs and experiences of those in cities are very different than those of people in rural communities, and the system needs to avoid being blind to either. I don't think that's entirely misguided but it smells a bit of special pleading; there are other ways we can slice the electorate that would likely lead to comparable (or larger) differences in needs and experiences, and we don't change the weights in light of that.
Arguably this inherently favors conservatism as passing no new legislation will keep things the way they are. Progressives will, in most cases, need to get legislation or referendums through to make meaningful changes to the current system.
Florida seems to have figured this out. This election there is a referendum to require voters to approve all new referendums twice to try to decrease the number of successful referendums.
The entire principle of popular sovereignty, as exercised through representative democracy, is that leaders are selected according to the wishes of the the majority of the people. Minority rule--no matter how it is codified or how long it has been in effect--is incompatible with this principle.
America can be either a country ruled by a Republican party answerable accountable only to rural interests or it can be a democracy. It cannot be both.
That's clearly not the case as many systems (not just the US) seek to avoid "tyranny of the majority" and to protect the interests of minorities. Canada's senate does not use proportional representation either - that avoids the country being run by Ontario and Quebec at the expense of the other 8 provinces and 3 territories.
The designs you argue against were specifically implemented to provide a system of checks and balances to avoid a simply majority from unchecked rule. And this is doubly true in the US, where it's a "union of states", not just one massive country. A lot of those rules were put into place in order to get the states to join the US because otherwise they would have had zero say in the affairs of the country.
Those checks you want to remove are not a bug but a feature.
The systemic disenfranchisement of the majority of the American population--through the electoral college, senate, and supreme court--is precisely why so much of American politics is broken.
Forcing the the majority to live under the rules set by a minority that has a completely different way of life does not lead to good outcomes.