Yes, voting for a third-party candidate is really a vote for Trump because Hillary Clinton is the only one who stands a chance to beat him. Johnson will not beat Trump. Therefore, voters must come together and understand that votes must be cast for Clinton. Trump is not fit to be president.
Voting for a third party candidate will essentially be a vote for Trump. Many in the Republican party have denounced Trump as an ineligible candidate already, but many Democrats are angry that Sanders did not win the primary. Third party votes will primarily be Democrats voting for Sanders effectually bringing down the overall percentages for Hillary and giving a vote to Trump.
This is a common refrain from both sides of the political aisle: don't vote for the third party, you will only help the other side. In reality, it appears that the Johnson-Weld ticket is drawing fairly equally from both the Republican and Democratic voter bases. Voters for Jill Stein do tend to come from the Democrats, but she is only accounting for 3% of the vote, at the very most. That difference is mostly offset by the slightly higher support that Gary Johnson gets from conservatives.
This is the first election in a long time where voting for a third party is a very reasonable option. There is a lot of disgust and dislike for both major candidates, and people should voice this with their votes. I personally believe that we should try to avoid a Trump presidency at all costs, and the best way to do that is to vote for Hillary Clinton, but if you vote for a third-party candidate, I am totally fine with that.