I responded to a similar point by not2b downthread. The following are some additional points I didn't make there.
To some extent the inequity you describe can be corrected by forcing particular methods for apportionment that can better prevent gerrymandering, and by increasing the size of the House to reduce the difference between the populations of the least and most populous districts. A certain amount of inequity of this type is, however, unavoidable in any representative democracy.
Also, this particular inequity is important to people only to the extent that what the Federal government does directly affects their lives. So an obvious way to reduce the impact of this inequity is to reduce the ways in which the Federal government can affect individual people's lives. The idea that Federal laws and regulations should be able to micromanage so many aspects of everyone's lives would have been horrifying to any of the Founders. Not only that, but it also disempowers people by making them much less aware of everyone's ability to find local solutions to local problems.
Another point to make is that the main problem with the Senate and the House has nothing to do with the inequity you describe: it is the simple fact that Congress has very low approval ratings but very high incumbent reelection rates. That means members of Congress are effectively never held accountable for bad policy decisions; they can continue to make them with impunity since they know they are not risking reelection by doing so. (For example, in all the furor over the CDC and FDA bungling COVID-19 testing, nobody to my knowledge has observed that the only reason the FDA had the power to prohibit State and local health authorities from developing their own tests is that Congress gave it that power, and legislation to rethink bad policy decisions like that is not even on the table.) That is not something that can be fixed by adopting a different system for apportionments.