"If the retailer takes so much of the money, why doesn't the publisher offer a direct online sales channel, where buyers can purchase the magazine? That way they cut out the middle man, and keep more of the cover price. Magazines seem to be one of the few things that you can't buy online - i wonder why that is?" - as Colin says, for specialist paper magazines, the overheads would be higher then the income. Digital is different as the process can be automated, but this requires an investment in IT infrastructure that might be beyond the smaller publishers. The model railway mags I work for do offer this service, but only for digital.
"Traplet had an online shop where you could buy individual copies of their magazines, both back copies and the latest issue. The main drawback was that it took around two to three weeks for them to arrive after ordering." - The important word is "had". If it was a route to riches, then they still would have one...