from the OED:
Early mod.E fuck, fuk, answering to a ME. type *fuken (wk. vb.) not found; ulterior etym. unknown. Synonymous G. ficken cannot be shown to be related.
and, earliest usage:
a1503 DUNBAR Poems lxxv. 13 Be his feiris he wald haue fukkit. 1535 LYNDESAY Satyre 1363 Bischops..may fuck thair fill and be vnmaryit. 1535-36 Answer to Kingis Flyting 49 Ay fukkand lyke ane furious Fornicatour. 1598 FLORIO Worlde of Wordes 137/1 Fottere, to iape, to sard, to fucke, to swive, to occupy.
the AHD says this:
ETYMOLOGY: Middle English, attested in pseudo-Latin fuccant, (they) fuck, deciphered from gxddbov.
WORD HISTORY: The obscenity fuck is a very old word and has been considered shocking from the first, though it is seen in print much more often now than in the past. Its first known occurrence, in code because of its unacceptability, is in a poem composed in a mixture of Latin and English sometime before 1500. The poem, which satirizes the Carmelite friars of Cambridge, England, takes its title, "Flen flyys," from the first words of its opening line, "Flen, flyys, and freris," that is, "fleas, flies, and friars." The line that contains fuck reads "Non sunt in coeli, quia gxddbov xxkxzt pg ifmk." The Latin words "Non sunt in coeli, quia," mean "they [the friars] are not in heaven, since." The code "gxddbov xxkxzt pg ifmk" is easily broken by simply substituting the preceding letter in the alphabet, keeping in mind differences in the alphabet and in spelling between then and now: i was then used for both i and j; v was used for both u and v; and vv was used for w. This yields "fvccant [a fake Latin form] vvivys of heli." The whole thus reads in translation: "They are not in heaven because they fuck wives of Ely [a town near Cambridge]."
and http://www.wordorigins.org has a similar, interesting discussion here:
http://www.wordorigins.org/wordorf.htm.
Personally, I wish there were more words that were so bad you have to encode them. :o
David