The word good is an adjective, and the word well is an adverb. The opposite of good is bad, and the opposite of well is badly. The link between the two words (and the difference between the two words) is thus more obvious in the negative form, and it seems to me that people don't confuse the negative words as much as the positive ones. (To make matters more confusing again, there's a word 'goodly', which according to Webster 1913 can be used as an adverb or an adjective. However, the use of the word as an adverb is marked as obsolete even then, and its use as an adjective is probably obsolete these days.)
It is possible to do something good badly - for example, rescue a person from a burning building but bang their head on the doorframe as you carry them out. The act of saving someone is a good thing, but the manner in which it is performed is bad.
Likewise, it is possible to do something bad well - for example, a robbery without any clues. To rob is bad, but the way in which this robbery is committed is good (or, at least, efficient).
Keeping these examples in mind can help keep the meanings of all the words clear.