The chakra runes definitely work on a variety of levels. My chakras give me roughly 3.5k or so bonus power overall, not a small amount.

Early on you can just stack all your best ones on whomever because you won't have quality in the variety of red/gold you have. However, once you get more and more you can easily fine tune them to be extremely fitting for each ninja. When I run Sailor Sakura I stack ninjutsu, defenses and secondary stats like recovery and damage reduction to make her heal more, survive longer and do more damage as she stacks passive. On my first slot I run primary stats and initiative because they are my frontline and combo starters. The bonuses that these chakras add is extremely useful and flexible so whoever told you they don't work or are useless is, in all honesty, an idiot.