I wouldn't be too concerned about viruses on an alien planet, because (unless one's premise is that life was seeded and transferred between star systems and life forms on the alien planet were very closely related to us), whatever genetic system aliens would have wouldn't be compatible with ours (viruses work by hijacking our cells' genetic machinery via either DNA or RNA). We'd be more likely to catch tobacco mosaic virus, since plants are going to be a closer genetic match to us than anything that evolved on an alien planet.
Could alien equivalents of bacteria or fungi be harmful to us? That's hard to say. It would depend on how similar our biochemistry was. Maybe they could grow on or in our tissues and cause infections, or even if they couldn't reproduce successfully in our bodies, they could possibly engender a massive immune response that would be worse than what they would be able to do to us on their own.
Toxins in the air or water that could cause problems with short or long-term exposure are another possibility. I remember reading a SF book where an alien "plant" species shed filaments that contained a lot of silicon. Exposure led to cancers (similar to ones caused by asbestos exposure) in colonists, so they lived under bubbles.
I think the only way to know for sure, once it was established that an alien planet had a compatible amount of oxygen in its atmosphere and a similar biochemistry to Earth's, would be to send probes to obtain air, water, and soil samples. It's possible we could miss something hazardous, though, if we don't know precisely what we are looking for (for instance, what an alien protein or pathogen that could elicit a dangerous immune response in Earth organisms might even look like).
Even so, I'm guessing human explorers would be cautious with exposing themselves unless they'd tested it on some earth organisms first. If there are ethical concerns with using vertebrate animals, might it be acceptable test on invertebrates, or even on tissues of various kind. It's possible that future biologists would be better at extrapolating system-level responses based on tissue studies than we are now.