Yes, it's algae and it's ruining your roof
Roof stains are caused by an algae called Gloeocapsa Magma. Once an algae spore lands on your shingles, it will continue to multiply and eat away at the limestone filler used in shingles today.
This feeding of your shingles will lead to premature loss of vital shingle granules and deterioration of UV reflecting protection, resulting in higher energy bills and eventually the need for a new roof.