There might be a few disgruntled republicans who are going to vote for the Liberterian canidate, but the majority of people who are voting third party are Bernie fans who are voting for Jill Stien. The truth is she does not have enough supporters, even combined with Bernie's supporters to win.
The theory that a vote for a third party candidate is really a vote for someone else is a theory that only holds water if we, as Americans, give it any weight. That means that if we vote for Clinton out of fear our 3rd party vote will count toward Trump, then several people that really wanted to vote for that 3rd party candidate actually voted for someone they did not want to win. If we all just vote for the person we really want to win, then there does not need to be a worry of what our vote would count as. I believe that the only true way to vote is to vote for the absolute best person we feel should be president and not get into the politics of taking votes from someone else.
No, a vote for a third party candidate is not necessarily a vote for Trump. Voting for a third party is voting for a third party. Also, by Obama's logic, it could also be a vote for Hillary depending on who you are talking to. For an undecided voter who leans liberal, who would otherwise vote for Hillary, it could be argued that that would be a vote for Trump.
In a two-party system, many times neither of the candidates seems an acceptable choice to the voter. In that case, it is good to show support for third party candidates by giving them your vote. If everyone feels that they have to stick to the main two parties, then it will always be hard to vote in real change. Imagine if a majority of voters was simply voting for one of the two main candidates when they really wanted someone else. This would undermine the whole purpose of democracy, which is to let the people pick the person they most want for the job.