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I think a rider's popularity plays a lot into how history judges. Indurain remains high on people's shit list for being an early adopter of EPO and time trialling to his TdF wins, Contador and Pantani are celebrated for their swashbuckling style, like Merckx.
Sky and generally successful British riders, like the Americans before them, are seen an interlopers by a lot of traditional cycling fans, who only seem to like riders from traditional cycling countries, and riders from Southern Europe best of all.
I think history tends to be kinder to them eventually. Merckx was disliked during his time and was infamously punched by a spectator in the 1975 TdeF for instance.
While Froome is winning everything and Sky are so dominant in the Grand Tours haters gonna hate. Not helped by Sky and Brailsford being so fucking awful at PR.