If by St. Thomas you mean Aquinas, then you should remove any reference to "microscopes" from your quote. he died long before they were invented. This is the crux of the disbelief in the literal transformation of the bread and wine into body and blood. Most people can accept it as a metaphore, but it does not look or taste like anything but bread and wine. Modern men and women rely on (scientific) evidence, consciously or unconsciously. Faith is required to accept the Eucharist as real. Pure faith is rare.
I believe that he meant something like "St. Thomas said this, and now with microscopes we observe that; without implying that a microscope was available to him.
Faith is required to accept the Eucharist as real.
Most certainly.
One point. The Real Presence is NOT antithetical to science. Quit the contrary--unlike past generations, we know that there is a deeper level of reality than appears on the surface. We know, for example, that bread, blood, and our bodies are comprised of atoms (mostly C, H, O, and N, with a bit of Ca, Mg, and some trace elements). These atoms are linked together in different arrangements to form the different substances. It is certainly possible that the process of transubstantiation results in a change at the deeper (non-chemical) level, with the atoms of the bread and wine being "swapped" for the glorified atoms that comprise the risen body of Christ.
This is not to say that the above "is" what happens in transubstantiation, but simply point out that a Real Presence is NOT wholly impossible of today's knowledge of science.