Why is "biblical" the only proper adjective to not use upper case?
Solution 1:
It appears that the central assumption in your question is questionable. Snailboat, FumbleFingers, and Sven Yargs have given examples to the contrary.
Wikipedia asserts:
An adjective can lose its capitalization when it takes on new meanings, such as chauvinistic. In addition, over time, an adjective can lose its capitalization by convention, generally when the word has overshadowed its original reference, such as gargantuan, quixotic, titanic, or roman in the term roman numerals.
FumbleFingers notes that at least one of these is true of biblical.
As to why biblical has become one of the proper adjectives that has lost its capitalization, the final, parenthetical, comment in your question is a large part of the answer--it is acceptable because it is commonly done. (My prescriptivist tendencies balk at this common fact without effect.) Perhaps the prevalence of the word and the book itself (which my hotel room nightstand comment referenced) has facilitated the "decapitalization" process.
Solution 2:
The Holy Bible - a.k.a. "the Bible" - is the proper title of a specific book; it has also gained a generic use meaning any comprehensive owner's manual or handbook, in which case it is not to be capitalized, e.g. "the investor's bible." The adjective for references to the Bible had always been capitalized - Biblical - conforming to standard rules of English (Italian cooking, Shakespearean tragedy, Homeric effort, et al) whereas when using it as an adjective referring to a handbook of comprehensive knowledge it would and should not be capitalized: biblical. As this generic application became commonplace, Biblical lost its capital B out of common usage; it became "commonly common." Language is a fluid thing, rules change as they gain acceptance. An example would be dangling participles. It is now fairly awkward to say, "Into which room are you going?" instead of "Which room are you going into?" In the same way, differentiation between Biblical and biblical has been lost, now depending on the reader's interpretation and context for clarity. It is more accurate and still acceptable to capitalize it, but no longer customary or required.
Solution 3:
Words that are commonly used and deeply entrenched in the culture tend to lose their proper adjective status. As in the case of french fries, roman numerals, venetian blinds, etc.