In dictionary, Chemistry means the complex emotional or psychological interaction between people (http://www.oxforddictionaries.com/definition/english/chemistry)
Seem the definition does not say that Chemistry is only used for romantic relationship. However, I often hear people uses "Chemistry" in romantic situation.
So, Is "Chemistry" used for any relationship or just for romantic relationship?
Can I say "I and my cofounder have a very good chemistry. We work together to grow our startup"?
"Good chemistry" is often used to mean compatible or simpatico. Romance is not required. From So You Want to be in Government?* by R. P. Nathan:
The term "chemistry" refers to the elusive quality of people who relate comfortably to you as the leader and to each other. Good chemistry sometimes involves people with similar personalities. It can also involve people with different qualities ...
*Emphasis mine.
I would say yes, it's fine. Of course it is the context that makes it so. You use the formal term, co-founder and you explicitly talk about work.
In basketball or any other team sport, teams that have great teamwork (who also happen to usually do the best) are said to have great chemistry. The word team can be inserted into it to make it team chemistry, but often times if you are speaking about a sport and say a certain team has great chemistry, most people should be able to understand what you are saying. For example, the Lakers had great chemistry back in 2010, when they won the championship, I hope this season they rekindle some of that team chemistry. Therefore to answer your question, the word chemistry does not solely pertain to romantic relationships and I have given another use for it.
