Clinton beat Trump in California by 4,483,810 votes, which is quite a different margin of victory than 2.8 million;  about 60% more.  She beat him in New York (both their home states) by 1,732,973 votes.  She got over 60% of the votes in California (our most populous state, and the sixth largest economy in the world), Hawaii, Maryland, Massachusetts and DC.  Trump got less than 40% of the votes in those locales and also in Rhode Island, Vermont, Illinois, Washington, and here Oregon.

See http://www.nationalpopularvote.com/ for a method to change the disproportion that Mr. Quirk's letter notes.  They propose a compact of states pledging their electors to the winner of the popular vote.  So far, eleven states, with 165 electoral votes, have enacted this into law, to take effect when a majority of electors come from members of the compact.

The Electoral College is only one of a number of undemocratic institutions in our government.  See also gerrymandered districts, and the US Senate.