Even though our kids are 2 and almost 4, we still call the pediatrician when something's going on that doesn't seem completely normal and let them be the guide of when our kids need to be seen or not.
Our daughter had all the typical signs of an ear infection yesterday (she's had 10 in 2 years + tubes), but it ended-up being nothing related.
Especially with your first child, they understand the protective nature of new moms. They'll let you know if you need to be concerned and what to look for.
As for pediatrician's offices being really germy - yes, they are. But, you have to be exposed to germs to build the antibodies to fight them. Most have masks, hand sanitizer, etc. to help prevent the spread of germs as much as possible.
Hope your LO gets to feeling better soon.