The thing is... 
Flags out: neutral to non Spanish viewers because flags don't mean anything to them, BUT NOT neutral to a large part of Spanish viewers because it shows a false, fabricated unicultural vision of Spain, the unitary vision of Spain is a right wing view and a clear residue of Franco's cultural genocide between 1939 and 1975, as much as Wikifrikiuser tries to obviate it.
Flags in: it represents a point of view that will not mind non Spanish users as they don't know what they are, and it represents a neutral and real multicultural point of view for Spanish viewers, not a biased and fabricated one as what some people here are trying to impose.
Conclusion: Flags in shouldn't offend anyone because it's the real thing, flags out offend as it's a lack of respect and authoritarism for supressing the reality