Why did my salsa go bitter?
While I haven't heard of it happening for the specific ingredients you list, yes, the blender can make stuff really bitter. 

There are two ways this can happen. First, a chemical reaction. A blender really churns the stuff through, driving lots of air bubbles into the mixture with some force. It also causes friction heat, especially professional grade blenders like vitamix. The heat, force and large reaction surface can cause the oxygen in the air to enter a reaction with the ingredients which doesn't happen when using a milder method for cutting up. Olive oil is a known culprit here, it usually turns bitter when blended, but it can happen with other stuff too. 

Besides oxygen, a chemical reaction can also happen between two ingredients coming from two different vegetables, which would not have been mixed well enough in the knife scenario to produce noticeable amounts of reaction product.

The second possibility is releasing stuff which would have stayed "packed" without the blender. A knife will only damage the plant cells at the cut surfaces, and a blunt knife, if used with a somewhat inefficient technique, might even break very ripe vegetables along the cell walls instead of cutting through the cells. If there are mini-droplets of something bitter within the plant cells, it is possible that the blender (which really cuts cells into pieces) released these things. On a more macro level, it is also possible that we are not talking mini-droplets, but just plant parts which didn't get cut with the knife. Stray pepper seeds come in mind: you probably didn't cut any with the knife, they tend to be pushed by a knife instead of cut when you are cutting the pepper. The blender pulverizes everything that hits the blades, including these seeds. 

I cannot know which of these is the most probable source, or which plant contained the bitter matter exposed/created by the blender. But the different methods of mincing vegetables are not equivalent, and can have very noticeable effects on taste and texture beyond the obvious chunk size. The bitterness you encountered is only one example. In general, use the method specified in a recipe. If you are not working from a written recipe, try out a few and see which works best.