If it's a simple trip through known and-or safe lands, sure.
But there's quite a few published adventures out there where the travel, or some of it, is itself an actual part of the adventure (or, in the case of the B-series module Journey to the Rock, is all of the adventure). And this is where the problems reside...how to make the travel bits challenging without spamming encounters all over the place, and without having to break consistency and use two sets of resting rules depending what the PCs are doing.
I would expect that any published adventure that incorporates travel as a significant part of the adventure would have encounter expectations that make sense for the area of travel. Like in Out of the Abyss, the PCs are fleeing through a demon infested Underdark....so the travel is very dangerous.
In Princes of the Apocalypse, the Dessarin Valley is described as a wilderness where creatures are common. It provides random encounter guidelines and tables. Interestingly, it has a table for Early Encounters and then a table for Later Encounters. The second includes more dangerous encounters in order to better challenge PCs as they gain levels.
Skipping, then: Old Man Willow, Bree, the pursuit by the Ringwraiths - and that's just to get to Rivendell. Then there's some more minor stuff, and Caradhras, and the Mines of Moria....
Sure, and the Barrow-Wight. But all of that is along the road from the Shire to Bree, right? Outside of the actual Shire.
And interestingly enough, for the most part, the road from the Shire to Bree would be perfectly safe for just about any travelers. It's dangerous for the Hobbits, though....kind of a different rules for PCs type of thing. Obviously, there is an explanation in the story for this....but that's something a DM can come up with in his game, if he feels he needs to justify the reason for the PCs having encounters. Things were different for Tolkien's main characters than for the background characters (based on the monster attractor you mentioned, mostly).
Skipping the travel bits, particularly through dangerous territory, means you lose quite a bit.
Sure, but I'm talking about skipping travel through non-dangerous areas. Travel in dangerous areas would not seem to pose a problem for the encounter expectations. For those who think that multiple encounter days, or multiple deadly encounter days break the verisimilitude of their world, they should not have such days in areas they don't want to be considered dangerous.
Well, it's a bit late to ask JRRT about that; but he did put some there.
Lanefan
Not really. The examples you gave are all outside the Shire. The only encounters taking place in the Shire are the few Hobbits who encounter the Ringwraiths asking after Frodo. Oh, and the scouring of the Shire after the end of the last book.
But I would expect most of us would view those as anomalies rather than as cause to change up a Shire Encounter Table to make it a very dangerous area.