It was more than simply a challenge to the church which was seen as a disruption to the civil order; many Anabaptists, with their radical dichotomy between the Old and New Testaments (wherein the Old no longer applied in anyway, as it was fleshly, carnal and pertained to earthly law) rejected the concept of laws entirely for the "spiritual man." This meant bad things for civil order and society. One only needs to look at the very real examples of Münster or of Thomas Munzer's rebellion if one is looking to understand the Reformer's fear of this sect.
This, of course, does not mean that every Anabaptist was a rioter; far from it. But considered broadly, these were not unfounded fears.