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Probably the major issue at the time was trust control of the railroads and concommitant use of shipping "rebates" on the railroads to basically rig the game by making sure transportation costs always favored the trusts. Since the railroad really was the only game in town in 1905, that tactic was a real choke-point for interstate trade.

Purists will no doubt say that it still wasn't any affair of the Federal Government, but one also has to put it in the context of a social tinderbox where there were very real anarchist and communist movements afoot in the country and there was no guarantee that republican (in the non-party sense of the term) sensibilities would win out in the end. Many of TR's actions were largely pragmatic efforts to relieve some of those pressures before the whole social structure fractured beyond repair, and he had as much if not more distaste for the attitudes of labor union extremists as he did for the Trusts.