I think subraces, as most often seen in D&D, are more like cultures, possibly with some element of subspecies in there. Neanderthal are, arguably, homo sapiens, so that fits both Frostburn and reality. In terms of the topic at hand though, it doesn't really matter. Whatever sort of grouping, social or biological, you see D&D 'race' as, it represents specific groups of people as having very distinct characteristics, some of which are positive, and some of which are negative. I think it is also pretty easy to see that the PATTERN of this allocation echoes, deliberately or not, patterns which are present in racist thinking in the real world (IE humanoids are generally depicted as having darker skins, primitive cultures, evil dispositions, violent tendencies, etc.).
What we name these groupings, and whether we consider them social or biological in nature, is not going to change any of this.