David Wasserman summed up how it happened succinctly:
As someone observed, if a state election gave the same disproportionate weight to rural areas as the Electoral College does in presidential contests, Roy Moore would be a Senator. But, so far, that's not how it works; majorities win.
Perry Bacon made a pertinent observation:
That's important. Democrats from very conservative states, like West Virginia's Joe Manchin, sometimes awkwardly try to shore up their elect-ability by adopting a few conservative positions. Jones didn't do that in the campaign, actually running as pro-choice, so he's not likely to do it in office either. (Except maybe on guns ...)
After all the discussion about how evangelical voters were sticking with the alleged-pedophile, Bacon also put out this chart (using PRRI data) showing the current national religious breakdown. Self-identified evangelical Christians make a lot of noise (and the label certainly fits most Alabama Republicans.) But the actual picture is more varied and getting more nuanced every year.