Yes, algae biofuel is generally good for ecosystems, because algae is an easy way to balance out pollutants. Algae blooms in the ocean are a good way to combat global warming and other things that humans do to pollute the world, without a great deal of inconvenience to humans. Algae is a way that humans can have their cake and eat it too, as it relates to the environment.
Algae biofuel is good for ecosystems because it is one way of promoting the use of vegetable oil for an example to fuel automobiles. Ecosystems can exist of any substance that is a part of that unique environment. Algae biofuel is a part of the fungus environmental family of ecosystems.