There's no extra security fee for one-ways vs. roundtrip. The TSA fee is $5.60 in each one-way direction domestically unless you have a layover of over 4 hours which will result in $5.60 for each segment. This is baked into the federal regulations. DL, US, and AA fares require a 4 hour connection or less to book on a single fare component on US 48 fares.You can still book longer connections domestically, it will just result in a separate fare on each segment. WN allows up to 8 hours. The feds don't care and anything longer than 4 hours domestically gets an extra TSA fee.

Fares between smaller, less competitive markets are a big part of it, but even larger ones can have cheaper roundtrip fare filings. For Example, UA SFO-MSP one way fares start at $304 Basic/$349 Economy while roundtrip fares start at $329 Basic/$419 Economy. SFO-DTW are similar at $304 Basic/$354 Economy for one-ways vs $349 Basic/$449 Economy for roundtrips. DL fares on SFO-MSP are the same and they are even higher on SFO-DTW. It's all about competition (or lack thereof as no LCCs compete on these routes). Roundtrip domestic fares require you stay until at least the first Saturday after departure (a roundtrip booking alone is not sufficient). If you primarily make shorter duration trips that don't meet these min stay requirements for roundtrip fares, you will just get one-way fares in each direction.

Some other larger markets from SFO with cheaper roundtrip fares vs. one-ways include ATL (another DL hub). There are some cheaper one-way fares in the spring on SFO-ATL, but summer fares are similar to DTW/MSP fares. Also, SFO-PHL route (AA hub) and SFO-IAH UA hub-to-hub route see similar one-way vs. roundtrip pricing to those mentioned above.