The Danish study refuting a link between thimerosal and autism was conducted at the University of Aarhuis, and published in at least two peer-reviewed scientific journals.
By contrast, the paper you cite does not come from a peer-reviewed journal - instead it was published in the house organ of the "Association of American Physicians and Surgeons", a fringe group which is avowedly anti-vaccination. And the paper's authors, the Geiers, are poorly regarded researchers working out of a private lab and making money from "expert" testimony which has been rejected in court as not meeting evidentiary standards:
The Geiers are also promoting chemical castration of autistic children through Lupron treatment, which is worthless. The mission of this board (Educating not Medicating) is contrary to the whole idea of giving children a powerful anti-testosterone pharmaceutical drug like Lupron.
Vaccination, on the other hand, protects children from dangerous diseases and avoids the need to give children drugs.