VT owns so much of its rail network because it acted early; they were the very first state to invest in self-ownership of its rail network. They bought the Rutland's property straight out of bankruptcy, so have owned the Western Corridor, Green Mountain, and Bennington Branch for 54 years now. They bought Lamoille Valley in '73 when the St. Johnsbury & Lamoille County went splat. They then snapped up the Montpelier Branch in 1980 when the Montpelier & Barre RR fell, the Wells River-north half of the Upper Conn River in '96 when CP got out, and the Wells River-south half of the Upper Conn River in '99 when Guilford got out. They even made an attempt to tag-team with VRS for the in-state portions of the Newport sub when MMA was being auctioned, but the bankruptcy court order that the whole MMA system's assets had to be sold intact to one bidder kept that from happening.
Buy low, buy low, buy low...notice a pattern? The only reason the state doesn't own portions of the NECR corridor is because the Amtrak eminent domain case against Guilford conferred ownership of Northfield-WRJ to the Central VT by federal action without VTrans having a way in. Otherwise they probably would've acted there too. CN's sales of the Central VT to RailTex and Grand Trunk to SLR's previous owners, and D&H's sale of CLP to VRS (done a year before Guilford bought D&H) were all done as conventional for-profit sell-high opportunities by Class I/II's to big holding companies, and not bankruptcy or suspension-of-service rescues like the others VTrans acted on. Plus, the Amtrak trackage rights on both of those private corridors gives VTrans a conduit for direct-funding improvements anyway, so they don't have the same motivation for self-owning those pricier lines.
Next opportunity for a buy-low is the inactive Mountain Div. from St. Johnsbury to Gilman, as Twin State/Lamoille Valley's trackage rights agreement with Pan Am expires 12/31/2018 unless representatives from LV's deceased owner's estate step forward to formally exercise a 10-year option. If that legally murky lease situation vanishes at long last, the state and PAR have expressed mutual interest in transacting now that it can finally be done drama-free. PAR wants it off the books so it doesn't have to deal with any more riff-raff way up there, and VTrans has a self-interest in controlling.