This is not a complicated concept ... sort of. There are two types of Alleles, Dominant and recessive. A dominant alleles is basically, well, dominant. It will only require one of your parent to have a specific trait for their children to have that trait. But a recessive is complete different, requires both of your parents to have that trait in order for the children to have the trait. So this is why some traits are more rare than other.
For example, a couple have a children. The father has brown eyes(BB) and the Mother has blue eyes(bb). Since brown is a dominate trait and blue is recessive, there is only a 25% chance for their children to get get blue eyes according to the punnett square. The reason for that is that the dominant trait does not need both letters to be capital in order to gain that trait, rather only one. However even though that the allele for the blue eyes is still in the children, but the dominant trait is the one that shows.