This question is actually in part based on something of a misconception regarding the origin of these names.

"John" is actually derived from Latin Ioannes or * Iohannes* in Latin and Iōannēs in the Greek. "Jonathan" is actually a variation of "Nathan", though obviously in modern times it's often shortened to "John". But the two names (John and Jonathan) have different etymologies. John had the meaning of "grace of God" while Johnathan was "gift of God". Both of these are ultimately derived from Hebrew, but the New Testament was not part of the original Hebrew Bible, so what you're seeing are names coming from Greek and Latin versions.

Luke is from Lucas like you say, but then like Ioannes, the Latin or Greek form is generally not the form of the name that was rendered into the English translations. Loukás would be the Greek equivalent of the name of Biblical Luke. Aristotle was likewise Aristotélēs. You'll see the pattern: The final ending (typical for Greek men's names) is being dropped in the English form. Same happens with Mark (Marcus), and, going back to John, the same thing is also happening. Matthew as well. It's coming from the Greek "Mattathias" or "Matthaios".

Thus all four names are going through the same pattern from Latin or Greek to English. That is, they're all losing the typical -*s ending as they are translated to English. The only difference with John is that it's not actually coming from Johnathan, but "Ioannes" or "Iohannes" as it's counterpart to Luke's "Lucas".

If you're interested, there are actually whole books devoted to biblical names. In particular you may be interested in The Transformation of Biblical Proper Names by Joze Krasovec, most of which you can find on Google Books.

Hope that helps clear things up.

tl;dr: John is from Ioannes; Johnathan is a different name altogether; Matthew is from "Mattathias"; All four name follow the same pattern of changes from their Greek/Latin forms.