It´s true not all the roots used in scientific nomenclature are latin, in fact a large amount is greek. However, those roots are latinicized, because scientific nomenclature is officially latin, therefore should be pronounced with latin standards and not greek.
I understand it´s a lot easier to pronounce scientific names as one would say the word in his own language, but i think it nullifies the basic purpose of scientific nomenclature which is to be exactly the same for absolutely everyone, with no possible mistake. As i said i generally find it really hard to understand an english speaker using scientific names, and i take for granted that any english speaker would have a hard time understanding me....which is a bummer.
You run into a whole new problem here: which Latin pronunciation do you use? Ecclesiastical Latin is different from Medeival Latin is different from Classical Latin. There were also dialects; an ancient Roman from Naples would probably have pronounced the "H" in Hyla, one from Padua would probably have not, and one from Rome itself may or may not have depending on his level of education (a well-educated Roman would be familiar enough with Greek to recognize Hyla as a Greek-derived word and pronounce it according to the koine standard, which did pronounce initial rough breathings, rendered in Latin as "H"). So...yeah. There's no simple solution.
I have found that somewhat normalized pronunciations arise within each group of individuals who typically talk to one another. American herpetologists have a different set of pronunciations from American herp hobbyists. I haven't been around zookeepers or professional herpetoculturalists much, they may have different sets as well. I would guess the same is true in other countries. So just listen to others in your group and try to use the same pronunciations they use. After all, communication is the goal, not correctness.