The process will not be truly carbon-neutral (for that, the CO2 would have to come out of the atmosphere, and if the algae could use only the limited amount of the gas in natural air, they would not grow fast enough) but each carbon atom will have been made to do double duty in a fuel before it finally escapes.
Woody biomass has been presumed to be carbon neutral because carbon emissions released by burning the wood would be taken back up from the atmosphere as new trees grew.