Lines in and out of Cardiff Central were closed early on Thursday morning after Network Rail's re-signalling work went on longer than planned.
They reopened at 08:15 GMT but disruption has continued to cause services to be cancelled or delayed.
Arriva Trains Wales hoped services would run on time by late evening.
Sophie Holley was waiting to catch a train home to Rhoose in Vale of Glamorgan when it was cancelled, so had to arrange a lift instead.
She said: "It's a bit of an issue, we've got to wait around in the cold now with a little one - it's a bit annoying."
It added there was still severe disruption to Valley line services, but it said trains to Penarth, Coryton and Cardiff Bay would be reinstated throughout the day.
Meanwhile, Maesteg services will start and terminate at Bridgend and a shuttle bus will run between Bridgend to Cardiff, calling at Pencoed, Llanharen and Pontyclun.
Replacement buses have been put on between Cardiff and Newport and tickets for Cardiff rail services will be accepted by Cardiff Bus.
Passengers took to Twitter to vent their anger at the delays.
Dan Walsh wrote: "Sheer madness at Cardiff Central today: not good enough @ArrivaTW @GWRHelp @nationalrailenq."
Rich Griff tweeted: "@GWRHelp been sat at a standstill outside Cardiff Central for over an hour. Anyone planned on travelling to Cardiff today. Don't bother."
Arriva Trains Wales said: "We apologise for this disruption and would advise all passengers to check before they travel at www.arrivatrains.wales/check for the latest information on disruption to services and assure them that we are doing all we can to get trains back on schedule as quickly and safely as possible."
Rail disruption continues across south Wales following earlier cancellations between Cardiff to Newport after engineering works overran.