I would like to mark a few points:
1- Yes, Y-DNA can be tricky regarding race classification for sure( in the case of Europe I prefer to call it ethnicities or phenotypes), since autosomal DNA equates more precisely with someone's phenotype. However, Y-DNA is incredibly useful in determining ancestrality, the original bearers of a language/culture and also in demonstrating the links between the peoples, in this case indo-europeans. Althought current european populations have a variety of phenotypes, they also have a variety of Y-DNA haplogroups, and at least to an extent and in ancient times this can be associated with certain migrating peoples. Naturally that nowadays these groups have mixed and one's Y-DNA doesn't tell the whole picture, but it is still very valuable in showing the original genetic links. Additionally, also to an extent the overall prevalence of the Y-DNA as well as of the M-DNA correlates to the ethnically dominant group in an area.
2-Phenotype and genotype are different. As some have already pointed out, some genes are recessive and not completely expressed, but they are there. Heterozygotic europeans can express recessive traits in their offspring depending on the genetic combinations that would happen marrying between europeans, if it were with asians or africans it wouldn't happen(comparing for example a brown eyed european reproducing with another brown eyed european or light eyed european, in both cases the offspring could have light coloured eyes), just a stupid example. But not only because of recessive traits that might be hidden, but also due to environmental adaption. One reason we could say that R1b people in southern Europe tend to display less frequently red hair and freckles is because the freckled skin of red headed people(unable to tan) is a genetic disadvantage in places like southern Spain, Sardinia or southern Italy, where these individuals would get skin cancer or other skin or sun related problems. The same reason why afghan and persian R1as have much darker skin tone than russians and ukrainians. The British Islands is another example, in this dark, foggy and poor in sun light environment, with a lot of humidity and forests, pale skin and light eyes are more likely to be widespread. Other things like diet and environmental conditions etc also influence overall body size, muscle mass, fat retention etc. Coon gave examples of how even newcomers in Australia had already different anatomies compared to englishmen in England, imagine that in the thousands of years of indo-european migrations.
with some reservations we can at least correlate some haplogroups with some peoples, with phenotypes a little bit less, but not completely impossible, at least as the "core" of a phenotype. For example, the classical scandinavian Nordic phenotype, lanky, narrow headed etc is mostly associated with I1 haplogroup(although I1 came from Central Europe originally, replacing the I2a1 scandinavians from the mesolithic, these newly arrived I1 were 55% western hunter gatherer and 45% neolithic farmers already, bear that in mind, that's why they brought agriculture into Scandinavia and this could also explain why they were more dolichocephalic than their I2a2 cousins). I2a2 seems to be related to Dinarics, and R1a seems to be related to what Hans Günther called the "East Baltids". The alpines are a little bit more tricky, R1b is very common in alpine dominated regions, but not always it equates with the alpine phenotype, what we don't know is if the alpine phenotype emerged in a combination of invading R1b indo-europeans with the local genes or if it was already there originally, very hard to know, since many original Yamnaya people were dolicocephalic(although we do see a sizeable minority between 15-25% of brachycephalic people, one stocky and shorter and the other taller, resembling much the dinaric and alpine types.) The R1a slavs tend to be brachycephalic, but alpines are not R1a, perhaps they are a combination of R1b and local I2, western hunter-gatherers. Hard to precise. Original anatolian neolithic farmers had already a consirable influx of western hunter gatherer as well, the Balkanic WHG had partially driven a wedge into Anatolia, so these populations are related since ancient times.