Most contractions in English are pretty straightforward: they are, they're; he would, he'd; is not, isn't; we will, we'll. The two words join together, minus a few sounds. Put it together, and shorten it up. What could be easier? But that isn't the case for "will not," which becomes "won't" instead of "willn't."
Why does the "will" change to "wo"? It doesn't really. Which is to say, we don't change it, our linguistic ancestors did. We just inherited it from them as a unit. But there was a reason for the "wo" in the beginning.
In Old English there were two forms of the verb willan (to wish or will)—wil- in the present and wold- in the past. Over the next few centuries there was a good deal of bouncing back and forth between those vowels (and others) in all forms of the word. At different times and places "will" came out as wulle, wole, wool, welle, wel, wile, wyll, and even ull, and ool. There was less variation in the contracted form. From at least the 16th century, the preferred form was wonnot from "woll not," with occasional departures later to winnot, wunnot, or the expected willn't. In the ever changing landscape that is English, "will" won the battle of the "woles/wulles/ools," but for the negative contraction, "wonnot" simply won out, and contracted further to the "won't" we use today.
When you think about what it takes to actually pronounce the word "willn't," this isn't so surprising at all.