Why does a base substitution in DNA not always result in the formation of non-functional proteins?

Protein structure is determined by amino acid sequence. Each amino acid is coded for by a triplet of RNA bases. These are transcribed from a DNA molecule. If a DNA base is substituted for another base, then the RNA triplet codon produces in transcription will differ. However as DNA is degenerate, there is more than one codon for each amino acid, so the amino acid coded for in the transcribed DNA may not be changed. If the amino acid now coded for by the DNA is changed then the protein produced will be non-functional as it will not fold correctly.