Flight passengers are checked by the airline, at least minimally, and there are also colocated border checks for ferries leaving from Calais so it's not really about the mode of transportation and it's the Hoek-van-Holland-Harwich line which is increasingly looking like an exception to a general policy of checking as many travellers as possible even before they actually set foot on UK soil.
The situation for flights is quite typical (other countries have similar rules) and sufficient to prevent large numbers of refugees from showing up at airports (note that this is mainly about deterring people with a real shot at asylum and most definitely not about spurious applications, which are actually somewhat easier to deal with).
The situation for trains and ferries leaving from France is somewhat unusual and has become a focal point because of the refugee situation and especially the tensions in the Calais area. The concern is that if those people did reach Great Britain, they would be able to lodge an application for asylum and it would be very difficult to remove them. This situation has been on-going for years (the first Sangatte “refugee camp” opened in 1999) and predates the 2003 Touquet treaty regulating these colocated border checks.
But then why make an exception for the Hoek-van-Holland-Harwich line while tightening controls everywhere else? I am speculating a bit here but I suspect it's simply that it hasn't yet been discovered by refugees (at least not in a big way) and/or the British tabloid press so everybody is happy with letting it continue as it always was. There are a few other loopholes (e.g. you could take a ferry to Ireland - with regular border controls on arrival – and from there ultimately cross the border to Northern Ireland) but as long as you don't have thousands of peoples at the gate as in Calais, it's not an issue.
Incidentally, note that ferries leaving from Belgium have no colocated border controls either and this has - to my knowledge – never been an issue until now, yet it was all over the news this week (at least in France and Belgium). So it might just be a matter of time before Hoek-van-Holland becomes an issue too.