OTH and LMT are the two Oregon UAX cities that seem to be odd balls in terms of allowable connections even from PDX to SFO. For example, you can easily fly UAX from PDX-EUG and then on to SFO for the same basic fare which adds EQMs and an extra EQS to your trip...ual.com will even allow you to connect in RDM or MFR if your heading east via DEN...but try adding a connection in OTH or LMT and the fare skyrockets, even if there is L, S, or T fare availability. I'd love to fly through OTH just for fun like I've done with EUG, but despite UA's VERY liberal connection rules for many itineraries, OTH and LMT don't seem to be part of the plan
I frequently fly to SFO from PHX. Because of my company's "lowest fare available" policy, probably 75% of my flights are PHX - LAX - SFO. Flying this route tends to save $250 when buying less than a week out. As fastair pointed out, it seems to be a supply and demand issue. Most of the PHX - SFO direct are almost always oversold. However, the PHX - LAX and LAX - SFO are rarely oversold.
I would do the route via LAX even if it was the same price as the direct...you're paying less money and getting an extra EQS...basically doubling your EQS # with each trip to SFO, not a bad deal.