The standard BibTeX bibliography styles impose fixed ideas about the capitalisation of titles of things in the bibliography. While this is not unreasonable by BibTeX's lights (the rules come from the Chicago Manual of Style) it can be troublesome, since BibTeX fails to recognise special uses (such as acronyms).
The solution is to enclose the letter or letters, whose capitalisation BibTeX should not touch, in braces, as:
title = {The {THE} operating system},
Sometimes you find BibTeX changing the case of a single letter
inappropriately. No matter: the technique can be applied to single
letters, as in:
title = {Te{X}niques and tips},
There's more on the subject in the
BibTeX documentation.