That does not mean there are people who cannot lose weight. I, my brother and sister are all skinny and we are triplets born from caesarean. If it had significant impact on weight then fair enough but clearly, it does not or we would notice everyone born via caesarian would struggle to stay skinny.
No one has said that we all have an equally easy time staying skinny but that far too many people lay blame at others for their own shortcomings.
The study seems does not point to any conclusion and since they did not measure the bacteria directly affected by different birth methods, even saying that the study suggests obesity of someone is linked directly to the way they are born, is a stretch.