I am glad the constitution protects the residents of those small states.
What are they being protected from?
The Senate can only be explained by looking at the historical context. At the time the Constitution was written there were 13 states that had recently gained independence from the British. The term "state" is no accident: these 13 former colonies each viewed themselves as independent sovereign nation-states at this point.
For a time they experimented with a loose alliance (organized under the Articles of Confederation) that was largely toothless because the only way it was empowered to do anything was through unanimous consent of all the states. Calls to improve this system led to what became the constitutional convention of 1787. Although the representatives to that convention largely understood and agreed that a stronger national government would bring some definite benefits, they also needed to convince each state to sign onto the thing.
One big sticking point in that negotiation was that the small states didn't want a purely population-based Congress where the bigger states could easily boss the smaller states around, while the bigger states did understandably think their larger population should be worth something. Our bicameral Congress is the result of a compromise here: one half is based on population, and the other half gives each state equal weight. It was thought that this would protect big states from bossing around the small ones, and prevent small states from ganging up to boss around the big ones, by ensuring bills would only become law when they were acceptable to both houses of Congress.
Furthermore only the House of Representatives was originally elected directly by the voters; senators were chosen by state legislatures to represent the interests of the state
governments. This was thought to protect the federal government from grabbing too much power from the states, since the senators had to answer to the state governments. This was changed by the 17th Amendment in 1913 to the current system where the people elect the senators directly. Incidentally the federal government is much more powerful now than it was in 1913. Coincidence?
All this is to say that the US would possibly never have formed a federal government at all if not for the assurance given to small states by the composition of the Senate that their sovereignty would be respected. Nowadays? I think the concern of bigger states overruling smaller ones is largely obsolete. As pointed out above, our smaller-population states aren't uniformly aligned with one political party or the other. The party divide is largely urban vs. rural at this point, and we have some small-population states that fall into each category. The result of this is that the Republican/Democrat percentages in the House of Representative really aren't all that much different from what we see in the Senate. What it does do is gives the voters of smaller states disproportionate say in most matters. Again, since there's not a whole lot of correlation between a state's population and its party preference we only see this make a difference in the Electoral College and such when the popular vote is extremely close anyway.
Still, it's perfectly fair to suggest that the concept of the Senate (and many of the other structures of our federal government) should be revisited from time to time to see whether they still represent what we want our government to look like. However with the Senate in particular there's a clause in the Constitution stating that "no State, without its Consent, shall be deprived of its equal Suffrage in the Senate." This is an exception to the general amendment procedure where consent of three-quarters of the states is sufficient. In the case of a reformation to the Senate to make it weighted by population, every state with a below-average population would need to agree to be "deprived" in this way. So...unless we throw out the Constitution and start over, the Senate is going to keep having two members per state.