I don't usually city hop, but one example where people have usually made a conscious choice to use rail is London --> Paris.
By air you fly from either Heathrow or Stansted or Gatwick or Luton (these are the usual 4) to CDG in Paris. The airports are not located within Central London and take significantly more time to get to compared to the major railway stations (King's Cross, Victoria, etc, I remember I took the Eurostar to Paris from KC both times I've been). CDG is also 30-40 minutes away by train from central Paris' Gare du Nord (main train station). Comparatively, Eurostar goes straight to Gare du Nord (or is it Gare du Lyon, in any case, you end up in central Paris).
IIRC the check-in timing for trains is also shorter. So while flight time is shorter (1 hour - 1 1/2 hour compared to 2 hour 15 minutes for Eurostar) you do risk losing some time in possible runway delays (more likely than train delays), more space is required since longer journeys in London means more vulnerability to the mercies of the London public transportation system and/or traffic.. And while the Eurostar probably costs more than a budget flight with taxes, you do have to pay for the train to and from the airports.
Most people find the Eurostar a safer bet, I guess.
You will have to do your research, I'm afraid.. Until you have a more concrete plan to make proper comparisons (if all these factors I've mentioned matter to you), there is no general right answer as to whether flights > train or vice versa. It really, really depends.