The simplest answer is that Europeans lived in dense cities with trade routes, and in close proximity to a variety of domesticated animals, which were (and remain) vectors and natural reservoirs for pathogens. This results in Europeans having better genetic and immune system resistance to prominent strains of viruses of the time.
As an aside, it is speculated that a virulent strain of Syphilis was indeed brought from the new world back to Europe http://archive.archaeology.org/9701/newsbriefs/syphilis.html, but overwhelmingly it was indigenous natives who would die and have extreme reactions to smallpox and other diseases that were generally less fatal to Europeans.
I'm not sure if this is the same thing as what you're getting at, but in the case of mosquito-borne diseases, colonizers in the sub-tropics and tropics died like flies up until the turn of the 20th century.
It was malaria and yellow fever in the Florida panhandle that led to the invention of air conditioning (as a means for Dr. John Gorrie to treat his patients' fevers).
During the construction of the Panama Canal, yellow fever killed at least 20,000 workers, one-third of the labor force, during the French attempt. When the Americans took over the project, the Isthmus Canal Commission took advice from a medical officer, Col. William Gorgas, who was a proponent of the new theory that mosquitos were somehow responsible. They agreed to spend $20 million on prevention, installing acres of copper screening, sending crews out to "fog" for mosquitos, draining wetlands and distributing free quinine.
And the CDC has the results:
The result of this malaria program was eradication of yellow fever and a dramatic decrease in malaria deaths. The death rate due to malaria in employees dropped from 11.59 per 1,000 in November 1906 to 1.23 per 1,000 in December 1909. It reduced the deaths from malaria in the total population from a maximum of 16.21 per 1,000 in July 1906 to 2.58 per 1,000 in December 1909.
Among the work force, the percentage of employees hospitalized due to malaria was 9.6% in December 1905, 5.7% in 1906, 1.8% in 1907, 3.0% in 1908, and 1.6% in 1909. Malaria continued to be a challenge throughout the entire construction program.
Prior to Gorgas' "kill the bugs" method, people thought malaria came from unhealthy vapors - mal aria, bad air. And it killed, according to those figures, more than 16 out of every 1,000 people in the isthmus region, at least.
Have you checked out this section from our FAQ?