SpaceX rockets don’t add Methane to the atmosphere. When you burn something, you’re not adding that thing to the atmosphere, you’re adding byproducts from the combustion, and Methane isn’t one of the byproducts of any rocket fuel.
Starship uses methane as a fuel, but that’s not at all the same thing. Methalox engines are one of the cleanest burning rocket fuels after Hydrolox. When burnt, methane just becomes CO2 and water vapor along with a bit of NOx (Nitrous Oxide, aka laughing gas, aka that boost you see in Fast and the Furious) as well.
Falcon 9 and Falcon Heavy are Kerolox (Kerosene, RP-1) engines. RP-1 is basically just a highly refined kerosene. When burnt, it will produce CO2, water vapor, NOx, carbon soot, carbon monoxide (which again mostly becomes CO2) and a little bit of sulfur compounds. The exhaust is nasty but it is not that different from what a normal internal combustion car produces. And even with the large amounts, it is still lower than what cars/trucks/SUVs output to get everyone in your city back and forth to work, the grocery store, and home on a daily basis.