No, they weren't. According to the latest results, Mrs. Clinton received 48% of the popular vote: that means that most voters didn't vote for her.
More voted for her than for Mr. Trump, but neither earned a plurality of the popular vote.
You mean a majority, no?
Clinton received the most votes, that is, the votes of most voters. The number of votes she received didn't represent a majority of the votes cast, but she still received the vote of most voters.
No, that's precisely not the case. She received the most votes, but not most of the votes. She did not receive the votes of most voters: 52% of voters did not vote for her. If we had instant run-off voting, we might know who would have come in first in a head-to-head matchup, but we don't.
Some folks like to blame third parties for their candidates' loss (Bush in '92, Gore in 2000, Clinton in 2016), but I don't think that's fair: we have multiple parties, and the parties are free to nominate the candidate most capable of winning the votes across America. People who voted for a third-party candidate didn't vote for either first-party candidate.