So the senate was once the house that would represent the states? Why was it removed, thereby reducing the autonomy of the states?
Answered in the link you quoted;
According to Jay Bybee, those in favor of popular elections for senators felt that there were primarily two issues caused by the original provisions: legislative corruption and electoral deadlocks. In terms of corruption, the general feeling was that senatorial elections were "bought and sold", changing hands for favors and sums of money rather than because of the competence of the candidate. Between 1857 and 1900, the Senate investigated three elections over corruption. In 1900, for example, William A. Clark had his election voided after the Senate concluded that he had bought eight of his fifteen votes in the Montana legislature. However, Bybee and Todd Zywicki believe this concern was largely unfounded; there was a "dearth of hard information" on the subject, and in over a century of elections, only 10 were contested with allegations of impropriety.
Electoral deadlocks were another issue. Because state legislatures were charged with deciding who to appoint as senators, the system relied on them being able to agree. Some states could not, and thus delayed sending representatives to Congress; in a few cases, the system broke down to the point where states completely lacked representation. Between 1891 and 1905, 46 elections were deadlocked, in 20 different states; in one extreme example, a Senate seat for Delaware went unfilled from 1899 until 1903. The business of holding elections also caused great disruption in the state legislatures, with a full third of the Oregon legislature choosing not to swear the oath of office in 1897 due to a dispute over an open Senate seat. The result was that the legislature was unable to convene for 53 days, and was forced to disband and call a new election.
If you want my modern take, there are two obvious problems with appointed Senators that make them a bad idea today. The first is the concept of having the "better men" of society in an upper house simply doesn't work. It's an attractive idea, but in reality having any politics behind such appointments corrupts both the appointers and appointees, while the institutional inertia required for such a system to work means that the "better men" are always behind the times. And that's ignoring the question of what qualifies someone as "better" (or good enough anyway).
The second is that state level elections will simply become a proxy for Senate elections, in the same manner that Presidential elections are proxies for the Supreme Court. There are whole blocks of voters who base their presidential vote on whether they will appoint liberal or conservative judges. Given that state level elections usually matter less to people than Senate elections anyway, putting such a significant power in the hands of state legislatures will swamp any local politics, utterly destroying the last holdouts of non-polarised, two party contests.
EDIT: I'd also argue that the representation of the states are still the same as when they were appointed by state legislatures. You still have equal representation despite population (two senators per state). You still have staggered six year terms allowing for institutional inertia. You still have all the power and authority of original Senate design. You still have them reflecting the general population of the state at large, just filtered through direct election rather than the elected state legislature.