I just started the game few days ago and i am on mission 5. I have no idea what FOB is but i guess its something related to mother base and it's resources?
Will i be affected if i start playing offline or it's too late for that?
Just play the game as it was meant to be played. The anti-FOBers are overreacting. The FOB is a net positive even if you get sucessfully invaded every day. There is very little in terms of managing it beyond what you do to manage the regular base because they are tied together.