Webster's standard response to readers inquiring about "nucular":
We do not list the pronunciation of "nuclear" as \'nü-ky&-l&r\ as an "acceptable" alternative. We merely list it as an alternative. It is clearly preceded by the obelus mark \÷\. This mark indicates "a pronunciation variant that occurs in educated speech but that is considered by some to be questionable or unacceptable." A full description of this can be found in the Guide to Pronunciation on our website at http://www.m-w.com/pronguid.htm. We are definitely not advocating that anyone should use the pronunciation \'nü-ky&-l&r\ or that they should abandon the pronunciation \'nü-klE-&r\.
To say "the word is spelled (x), and therefore should be pronounced (y)" doesn't make any sense. Spelling is not a legitimate basis for determining pronunciation, for the following reasons:
1) English spelling is highly irregular. For example, "move", "dove", and "cove" are spelled similarly but pronounced differently. Likewise, "to", "too", and "two" are spelled differently and pronounced the same.
2) English spelling is frequently based on factors besides pronunciation. For example, the "c" represents three different sounds in "electrical", "electricity" and "electrician", but is spelled the same in all to show that the words are related.
3) Most importantly, spoken language is primary, not written language. Speaking is not the act of translating letters into speech. Rather, the opposite is true. Writing is a collection of symbols meant to represent spoken language. It is not language in and of itself. Many written languages (Spanish, Dutch, etc.), will regularly undergo orthographic reforms to reflect changes in the spoken language. This has never been done for English (the spelling of which has never been regularized in the first place), so what we use for written language is actually largely based on the spoken language of several centuries ago.
All of the entries in our dictionary (pronunciation, meanings, etc.) are based on usage. We have an extensive collection of files which date back to the 19th century. Language is changing all of the time in all respects, and any dictionary which purports to be an accurate description of the language in question must be constantly updated to reflect these changes. All words were pronounced differently at some time in the past. There is simply no scholarly basis for preferring one pronunciation over another. To not list all pronunciation variants would be irresponsible and a failure of our mission to provide a serious, scholarly, record of the current American English language.