How can I understand the distinction between public goods (non rivalrous and non excludable) and primary goods (as defined by John Rawls)? I...

Pollution would be a "negative public good", sometimes called a "public bad"; but that's not really the fundamental distinction here.

Public goods, as you note correctly, are any goods that are nonrival (they can be used by many people at once) and nonexcludable (it's difficult to stop anyone from using it if they want to).

Public goods can be directly compared to private goods, which are typical goods that are rival and excludable (e.g. shoes), club goods, which are nonrival but excludable (e.g. nightclubs, toll roads), and common goods, which are rival but nonexcludable (e.g. water supply). Common goods are really the worst; they are what give us the Tragedy of the Commons.

These are all economic concepts with clearly defined descriptive meaning.

Primary goods are a more philosophical concept with a more normative sense behind them; John Rawls uses the term to describe anything that is intrinsically valuable to humans, anything that would be desirable from the "original position" behind the "veil of ignorance" in which we know nothing about what sort of person we'll be.

He gives some examples such as intelligence and health; presumably everyone wants to be intelligent and healthy, there aren't a lot of people who want to be stupid and sick.

He also considers rights to be primary goods; everyone wants to be free, everyone wants to have a say in their government.

Examples of things that would not be primary goods are anything that varies based on culture or taste. Not everyone wants to eat vanilla ice cream, some people don't like vanilla; not everyone wants to live in a big city, some people prefer the countryside.

The idea is that primary goods are what we should be trying to get if we're in the veil of ignorance, while goods that we'd only want once we knew something about ourselves or our position in society would not be primary goods. We decide how to make a just society under the veil of ignorance, so only primary goods are important in that judgment.

You're right that a lot of primary goods are public goods---fresh air, free speech. But some primary goods are private goods---Rawls includes wealth as a primary good. Still others are hard to place, like health: Is health rival? Is it excludable? Healthcare seems like mostly a private good (a doctor can only treat one person at a time, and can always choose not to), but then there are considerations of public health (such as vaccination and herd immunity) that make it more like a public good. But health is definitely an example of a primary good in the sense Rawls intends.

To be honest, I find this concept a bit tendentious. It's pretty hard to clearly define what everyone would want, especially in some deep sense of fundamental desirability to all rational persons. Maybe not everyone wants a say in their government, for example; perhaps some would prefer to be left alone and let people who know what they're doing make the decisions. That's not incoherent at least, even if we might disagree with it. Nor is it clear to me that a society could deny people taste goods at will---banning chocolate, say---without being unjust or imposing upon liberty.

Indeed, if that example seems silly, try this one: Banning homosexuality. This is something a great many countries around the world have done, and sex with people of the same gender can't be a primary good since not everyone wants it---but it certainly seems like a fundamental violation of liberty to ban it. Maybe we can justify this by some broader primary good like love or sexual freedom; but at least for me it raises some serious doubts about whether primary goods are doing any useful work for our judgments about justice and injustice.