That doesn't mean their vote should count more than people in the cities.

The problem is that they get a double bonus on the national stage because of the Senate AND the disproportionate representation in the House due to it being capped at 435 members. This means they have an outsized influence on all three branches. Electoral College for president, Senate AND House because of the House being capped at 435 members, and the nomination process for justices including SCOTUS.

If the House was truly proportional to population it would be better. Making the second place in the presidential election the vice president again would be even better since they can break the ties in the Senate. If the presidential election was changed just straight up popular vote that would make it so the only advantage for a state is the Senate and that would be plenty.