Why is the percentage similarity in the gene always lower than the percentage similarity in the protein for each of the species?

Recalling to how DNA produces RNA, the synthesis of making RNA involves the process of using uracil not thymine. Synonyms in the genetic code exist and some species only use one synonym to get the same amino acid. The reason why the percentage is low in gene is because it does not involve a lot of processes compared to the proteins which undergo mRNA and tRNA to be coded as amino acids.