I recently tried nattō on top of rice. All I tasted was bitter. I didn't get any nuttiness or saltiness. The natto was also generously garnished with scallions, maybe that was a major bitter contributor. What is nattō alone supposed to taste like?
Natto shouldn't be salty by itself, because salt kills the culture that grows on the soybeans. Salted soybeans are fermented into miso; unsalted ones become natto.
Normally, you'd season the natto with some combination of strong Japanese-style mustard, soy sauce, scallions or Japanese leeks, and maybe grated nagaimo if you want an even more mucilaginous texture.
The flavor of natto is fairly mild; the aroma is certainly stronger than the flavor itself, and is reminiscent of bleu cheese and sweat. I'd say it's slightly sweeter than a boiled white soybean would be, but it's possible than an objective measure of sugars might disagree with me there.
Soybeans are very mildly bitter on their own. Tempeh, a similar cultured soybean, tends to be slightly bitter, but I would say it's not a very pronounced trait, if at all present, with natto, as most of the bitterness seems to be removed by the fermentation.
Assuming you started with frozen natto that wasn't freezer burned that you allowed to reach room temperature, or fresh natto that wasn't excessively old, I would simply mix the natto aggressively in a small bowl for a few minutes until the mucilaginous strands form. Then season as desired.
If you're expecting a surprising flavor, by the way, you may be disappointed in nattō. Japanese cuisine emphasizes contrasting textures much more than aggressive flavors, which is to some extent why so many dishes are seasoned only with varying proportions of salt, soy sauce, sugar, sake and mirin, and vinegar (su).
But if you're experiencing an unusually bitter natto, that sounds like a problem with the natto that you purchased, rather than the ingredient itself.
I have tried a number of types of natto, and the smell and the texture are usually much more prominent than the taste. Recently I had to describe it to a person that had never tried it, and I said something like "feels like runny, gooey old socks, with a hint of raw potato - worth trying once".