If you read this article you’ll see that the best way from BER into Berlin is to take the “regular” train which is a combination of standard Intercity services, regional services and the new FEX service which are timetabled to give a rough 15 minute frequency through the day. Despite the IC and FEX labelling, all services are included in the standard city pricing so will cost €3.60 each way, same as the S-Bahn. But the normal trains take 27-35 minutes and the S9 will take almost an hour.
https://www.europebyrail.eu/berlin-airport-opening-ber/