I find a certain phrase in a particular question very offensive. However, I can't flag it as "offensive" like I can a comment. Is this by design? What should I flag it as instead?
If a particular phrase in a question offends you, you can edit it out from the question as long as you don't change the original meaning of the question itself. For example, in this question, you might change the phrase
It's not merely supernatural which has a connotation of being non-existent, like God.
It's not merely supernatural which has a connotation of being non-existent, like ghosts.
It's not merely supernatural which has a connotation of being non-existent.
This way, the original poster's intention of finding a word that didn't work is preserved but the phrase that could offend more religious users is stricken out.
If, instead, the entire question offends you, there is a flag as offensive option on any question or answer. To do so, click flag, then select it is not welcome in our community. This reason denotes that a question is "offensive, rude or hate speech".
If it is possible, however, to salvage the question I would recommend making the edit. That way, the useful part of a question stays on the site.
One key distinction to note is that there is, as Mitch pointed out, a difference between talking about something and using it. For example, questions on profanity or other offensive terms are often on topic, but using them in another context (say, swearing at someone) is not necessary to the question. The former should stay, the latter probably not. Talking about God when it's part of the question, then, is valid material.
The flag you are looking for is "it is not welcome in our community", which has the following description:
This question contains content that a reasonable person would consider offensive, abusive, or hate speech.
Click on the "flag" link, and you will see the dialog box the previous screenshot shows.
I took the screenshot from this site, but the main site shows the exact same flagging reasons.
Notice that the flagging reason doesn't allow you to specify which words/phrases are considered offensive, but as the flag description says, "this question contains content that a reasonable person would consider offensive"; the offensive part would be easily caught by who reviews the flag.
If the post offends you directly, for example because it contains an indirect reference to you, such as in "who said [phrase you said in an answer of yours] would not agree with my answer, but he is an idiot," then you might want to flag the post using a custom reason. However, in general I would suggest using one of the pre-defined flag reasons, as those are visible to 10K users, who can flag the post as offensive too. Flags with a custom reason are visible only to moderators, which means only moderators can resolve them.
I would not suggest editing the offensive part from the post; this could cause editing wars. It is better to get users to agree about the post being offensive; at that point, moderators can take the necessary actions, if the post was not flagged as offensive from 6 users.
To answer your specific question: you can flag a question as offensive:
it is not welcome in our community
It's not merely supernatural which has a connotation of being non-existent
, like God.
I consider the original sentence unwelcome on English.SE, and consider your edit equally unwelcome. I do not mean to be rude or unfriendly: just direct.
The owners of StackExchange intend SE sites to be “libraries of high-quality questions and answers, focused on each community’s area of expertise.”³ As the owners they have every right to choose what (and what not) to publish. English.SE “is for linguists, etymologists, and (serious) English language enthusiasts”. So Q&A on English.SE is limited to topics relevant to that expertise. And the FAQ clarifies what that means: word choice and usage, grammar, etymology, etc.⁴ Anything outside that realm is off topic and unwelcome.
Questions are welcomed even when they are offensive (to some). The owners of SE have repeatedly made clear that any text is welcome at English.SE regardless of its nature, as long as its presence there legitimately serves the community. (With the exception that titles of questions need to be rated G to prevent the site being flagged by third party content filters.)
Evan Carroll⁵ was wrong to post the original sentence not because it’s offensive but because it’s off topic: it is a rant disguised as part of his question. Evan’s defense of the sentence just underscores his intention to engage in polemics, not make a linguistic argument. The sentence is linguistically indefensible: it is factually untrue that supernatural has a connotation of “being non-existent”, any more than my grandchildren does: they are nonexistent, but that just so happens. It is not in any way connoted by the term.
You were wrong to edit the question the way you did. You explained your edit as “removed offensive phrase”, and your sole justification turned out to be that it was you who found “a certain phrase … offensive”. Where you went wrong was in using your personal level of offense as a touchstone for whether content is welcome in our community. The standards are community standards, not yours. Ironically, your edit contributed nothing to the quality of the question: you removed “God” but not the polemic. And, if allowed to stand, your edit might encourage more people to substitute their own personal standards for those of the community.