This is nothing to do with grammatical rules. Idiomatically, we usually add the indefinite article if we're going to use only before few, but that's not a hard-and-fast rule. From Google Books:
but only few are 7,310 hits
but only a few are 176,000 hits
I can't see any difference in meaning - with or without the article, with or without the word only, it nets down to the same thing. But it's worth pointing out that if we discard only and focus on the verb to be, the preference is not to include the article:
but few are 2,280,000 hits
but a few are 905,000 hits
I've no evidence to back me up, but I suspect the modern trend is probably moving towards including the article. The high number of hits for my example #3 are probably much influenced by long-established forms such as many are called but few are chosen.