If you align most with the libertarian party, and want a libertarian to have a shot at winning, maybe not this election, but eventually. Then voting for Johnson is not throwing away your vote. If he gets 8% of the vote this year, the libertarian party gains a lot of attention and will have a better probability for libertarians to be elected in future elections.
Also, the president doesn't have a magic stick that he can wave to pass whatever he wants through congress. He can at best veto bills that get through congress.
I believe a Johnson presidency would mean many vetoed bills that would increase spending, less military involvement in foreign countries, reduction or complete removal of the NSA spying on US citizens without due process, and for him to sign anything that would give us more individual freedoms(or less laws) including making abortions more available, less gun laws, legalizing marijuana and potentially other drugs, gay rights, etc. I also expect him to be more open to each political party and for them to be more open to him, for instance, not veto a bill just because it's not from his political party, or for congress to meet with the potential supreme court justices that he nominates.