Yes, primaries in United State's presidential elections give unfair advantage to the incumbent president. The standing president does not need to run against other members of his party in primaries. He is generally accepted to be his party's candidate, while the rival party much sift through multiple candidates and may not be united behind their final choice.
While the incumbent has no running mate in the primary, generally, the other side has two candidates making each other look bad. In addition to this primary competition, many voters may be upset when their choice for the primary does not win, and decide not to vote in the election. Primaries do benefit incumbent presidents.