Just going to throw out there that it's 10 miles from downtown Portland to downtown Vancouver via BNSF. If you could actually get a train to run 60 mph – which doesn't seem like that much of an ask! – for that length, that's a 10 minute trip.
BNSF is not going to approve commuter rail runs, especially over one of its chokepoints. Not unless you throw a ludicrous amount of money for those slots (which is what Seattle has to do in order to buy more commuter rail trips).
OK, another
actually: Except for the section between Union Station and Vancouver, all of the PDX-area trackage belongs to either UP or regional Portland & Western (except for the municipally owned Steel Bridge & approaches trackage, which is owned by the Port of Portland). Most BNSF freight traffic from the east turns north at Vancouver (around the non-passenger side of the wye), where there is a major terminating yard, particularly the most common stuff -- Asia-bound grain shipments, which head up to either the Port of Kalama or all the way up to Tacoma, or container traffic, mostly bound for Tacoma and Seattle (BNSF uses the Columbia River route, although longer, to avoid the Cascade Tunnel chokepoint; most Seattle-bound or originating containers use that tunnel under Stevens Pass, while Tacoma container trains (which comprise about two-thirds of the total container cargo) are split about evenly between the northern Cascade and the southern Columbia routings. The Columbia route also has the advantage of fewer and much more benign grades. On the Portland side of the river, the port facilities are primarily served by UP, whose tracks lie on the Oregon side. The primary freight traffic using the Columbia River bridge is comprised of UP "run-throughs" to their relatively small Seattle facility (UP has trackage rights on BNSF as far north as Centralia, where they access their ex-Milwaukee tracks into Seattle); these are only one or two in each direction daily. BNSF traffic usually comes from their ex SP&S line downriver toward Astoria (it used to go all the way into that town, but now terminates at a lumber facility about 10 miles east along US 30); usually one train a day of forest products; also, there are transfer runs to the UP "Brooklyn" yard SE of downtown PDX for freight heading south toward California. UP doesn't use BNSF's St. John trench; they have their own mile-long tunnel under North Portland to access their main yard on the east bank of the Willamette north of the Steel Bridge. So the BNSF line over the rivers from Portland to Vancouver is hardly a major freight chokepoint -- but, as Bruce states, they
have become quite accustomed to "cashing in" on allowing commute traffic to use their rails.
Because of Seattle's topology there are relatively few useful rail lines in and around that area that lend themselves readily to commute purposes (Lake Washington is a formidable obstacle to any efficiencies regarding a E-W regional commute), and except for the Puget-hugging BNSF line, limited practical ways for a rail line to head north (the old NP line through the U of W campus and heading through Kenmore was pulled up in the early '80's; local NIMBY sentiments were largely responsible for that loss). Essentially, BNSF, at about 80% of the total trackage game, has Seattle at a disadvantage -- their predecessors (NP & GN) got there well before the population boom and secured the major points of egress. OTOH, Portland is relatively wide-open; originally served by 3 major railroads (UP, SP and NP/GN subsidiary SP&S), they effectively split all the available egress points. From what I've heard (and locals can and should chime in about this) there's a rudimentary rail (not LR) commute system connecting Portland, Lake Oswego, Tigard, and Beaverton, using tracks that snake through various valleys to circumvent the West Hills. These tracks are mostly owned by P&W, a regional freight hauler much more open to the commute concept (hell, they let Doyle McCormack, the locomotive restorer responsible for the SP Daylight and other historic steam, run excursions over their tracks on a regular basis). But UP hasn't acceded to any commute entreaties to date besides what's currently provided under the Amtrak aegis -- they, more than BNSF, are the party that has kept commute rail from being deployed south and east of town. And unlike the Caltrain service in the Bay Area and much of Metrolink in greater L.A., where the operating agency owns much of the trackage as well, neither UP nor BNSF has any intention of selling any of its tracks to any public agency. But historically BNSF
has been more open to commute rail operations over its tracks (if compensation can be arranged) than has UP (although the latter grudgingly does allow Metrolink to run its Riverside line over their freight corridor). UP is notoriously hard-nosed about its dealings with the outside world; the chances of Portland-area "heavy rail" commute service expanding beyond its present state are slim indeed.