It has long been known by agents that the only way to make a really safe connection (safe in terms of not having to worry about it) between two or more flights, is to make sure that all the flights are on the same booking (in the trade, known as a PNR or Passenger Name Record) AND that all the flights are on the same ticket. I say "and " because having all flight on the same PNR does not always mean that the flights are all on the same ticket.
If you book with a proper agent, then you will be able to ascertain that all you flights are on the same ticket and PNR; if you book online... well, anything could be the case.
This has been a big issue for the low cost carriers (LCC's). In the quest to find extra business, having two flights being treated as two totally and wholly separate travel "events" is, to put it mildly, a bit of an issue. Some LCC's are trying to find ways of doing this for their own airline's flights - but what about if you wish to transfer from, say a RyanAir flight to an Easyjet flight? Or an Allegiant Air flight to a Southwest Airlines flight?
Launched to very little fanfare (and taken even less notice of by the UK Travel Media) some while ago, was "Gatwick Connect" which service, goes in some measure to find a solution to the issue - that is, a sort of insurance policy to guard against missed separate travel event flights. For the sum of £12.50, Gatwick Connects offers, if you miss the connection, to put you on the next flight for free (they also offer a few other bits and bob's ... but this is the main element) The only other similar arrangement I have seen so far is at Milan Malpensa Airport, with ViaMilano. Both these services offer face-to-face customer support at their respective airports.
On the face of it, this is a very worthwhile and incredibly useful thing to have. There are certain things you have to do, none the least of which, is book *all* your connecting flights on their website. This is understandable as they wish to make sure that enough time is allowed for any connection in the first place. The devil, as per usual, is in the detail and you do need to read what is excluded. Problems (aka "missed connections") caused by strikes, storm, snow, volcanic ash and the enigmatic "airport asset failure" are excluded. Quite what this last element is supposed to cover, I am not too sure - so it is well worth asking. That weather is effectively excluded means that this sort of concept has still some way yet to go. That said, it is a helpful step in the right direction.
Needless to say the *yawn* marketing types have got hold of the concept and gave this a fancy name - "self-connect" and the usual culprits in the travel technology world have fancified a new name as well; they call it "discreet choice modelling". No doubt someone will be able to use this to grace many a travel tech convention!
Having said everything above, let me make a few things clear. This system is by no means perfect. The exclusions to the policy are a huge downside and though I am sure the concept will be developed into something more user-friendly and probably re-surface as a basic travel insurance type policy, it is a move in the right direction which I feel LCC's would be wise to embrace and encourage.
At present, the only way to really guarantee a hassle-free connection is to make sure all your flights are on the same PNR and on the same ticket. Remember the nature of online booking is such that you seldom get to see your actual ticket (in the background of each and every booking, irrespective of how booked and with whom, there is an actual ticket). If your (online) ticket is there, then it is often hard to find - and even if you do find it, you need to know what you are looking at.
Visiting your travel agent is the only sure way of knowing exactly what you have booked and what you have paid for and the only sure way of making sure that you fully understand what the ramifications are of a particular booking.
The message still remains: If you need to travel from A to B and have to go via C and possibly D - visit your travel agent.