Fares just are more expensive in Cork
Dublin-Skerries (31km): €8.00 rtn
Cork-Mallow (32km): € 11.40 rtn
Although, for some reason Cobh is cheaper than Midleton, even though they are almost the exact same distance from Cork. I know Irish Rail like to pretend that the reason for higher fares is because of things like double-tracking, but Cork-Cobh is double tracked, while Cork-Midleton is single-track beyond Glounethaune.
I guess unless a local politician wants to make an issue of it, fares are likely to stay higher in the Cork region.