It's not necessarily negative but it might show some insecurity towards the future, depending on what you're talking about. You think it's good so far but you're unsure about how it will turn out later on.

Yes, it means that up until this point everything is going well. As for the connotation, it really depends on the context in which you use it. You could use it cautiously optimistically or neutrally. Stating that things are going well is not exactly pessimistic and you would usually not use "So far so good." in such a context. Cautious optimism: Trying something for the first time, such as sewing. You are stitching and the instructor/your grandma/your mom/someone asks: "How is it going?" You: "So far, so good." (In a tentative voice) could be cautious optimism. If you were more absorbed in your work and were replying more curtly, it would come off as a neutral statement.