Remember, JNU is only 30,000 or so people. While YVR is a relatively popular destination out of Juneau, that still only translates to 4-5 people a day, maybe 10/day during the summer. FAI then PDX would make far more sense for N/S service out of Juneau.
Its not so strange that SEA is the gateway to Alaska vs. YVR. Up until the last 10 years or so air service between the US and Canada was very restricted, so what service there was out of Vancouver was focused south, not north. Plus it makes more sense to transfer in another US city (SEA) vs. a foreign port (YVR) when making your way between two US points.
For the record, besides Alaska, Juneau has been served by PanAm, Wein Air Alaska, Western (once in the 60s/70s then again in the 80s), Delta (after the purchase of WA) and MarkAir. PanAm and Western were required to give up the market by the CAB, and all of the others dropped Juneau after varying amounts of time. Air North has had service to YXY for several years, but only a couple of times a week. Canadian North has never served Juneau.
Sorry for rambling, but I got my start in the industry in Juneau, so I'm sorta fond of the town.
"The two most common elements in the universe are Hydrogen and stupidity"