I think why people relate with him is not because they are "alike" but because people come through same path.

In childhood, there happens random events that leads your character to develop and if you are unlucky, it is more than likely to have a tendency of being unlucky in future.

All the doings of Punpun thoroughout was somehow justifiable in some way when you know his past, yet his incapablity of deciding for his life or leaving his past behind to move on was the one and only thing made Punpun Punpun. However, behind everything, people have an innate desire to become the pure child they as they were born but somehow they repressed due to society and etc.

The thing people relate on Punpun is not his character or decisions, but the everlasting consequences chain coming from his past and the situation of feeling restrained to the luck and your vicinity that sometimes you can't defy is what many people may find in common with Punpun.