Apart from that being a fallacy - the properties of the parts are not necessarily the properties of the whole - it neglects that the arrangements of those mindless atoms have been honed by billions of years of evolution in a world where valid decision-making and accurate assessment of reality tend to enhance survivability.
In contrast, if your brain was the creation of a tyrannical deity who demands his subjects worship him or he’ll torture them for all eternity, you definitely would have no reason to trust your thoughts.