I would support a system based on proportion of statewide popular vote (i.e. if you live in a state with 10 EV's, you get 1 EV for each 10% of the vote you get, rounding to the nearest multiple of 10%), simply because there are many states (PA, IL, OR, WA, etc.) where non-urban areas typically don't matter in terms of deciding who gets a state's EV's because of the domination of a big urban area (Philadelphia/Allegheny County, Cook County, Portland, Seattle/King County) . Just because you live in a rural area doesn't mean you don't deserve representation in the electoral college. With the current system, you have a situation where (for instance) Washington State's electors are essentially representing the interests of King County, while the rest of the state gets no representation whatsoever, and that just doesn't seem right. (For what it's worth, under this system, Obama would have won 276-261 in 2012, with 1 EV for Gary Johnson in CA. Obama would have 51.3% of the EV's to Romney's 48.5%, for a 2.8% Obama EC margin, which is pretty close to his 3.9% margin in the NPV.)
However, a system like Nebraska's is not something I support, as it would only make the problem worse. Democratic governments gerrymander districts for democrats, and republican governments do the same for republicans, so you'd essentially be leaving the EC open to the gerrymandering that has already plagued the U.S. house. This goes far beyond simply giving rural areas represenation, and instead actually skews the results so that it misrepresents the interests of the nation as a whole and has a much higher risk than the current EC of electing someone who lost the NPV (If NE's system was used nationwide, Romney would have won 274-264 in 2012's EC. This comes out to 50.9% of the EV's going for Romney to 49.1% for Obama, or a 1.8% Romney EC margin, which is off, quite significantly, from Romney's 3.9% loss in the NPV.)
The main problem with this plan is that electoral votes are not actually proportionally distributed across the country by state population. Under the current system, a citizen of Wyoming is disproportionately represented in the electoral college compared to a citizen of California (1 EV for every 194,717 people vs. 1 EV for every 705,500 people). Distributing EVs proportionally within each state would exacerbate this problem. Based on 2012 vote totals, under such a system a third party candidate would have had to get around 237,000 votes to get one of California's 55 EVs, while in Wyoming they'd only have to get 83,000 votes in Wyoming to get one of its EVs. So branding such a plan as a "Proportional" system is really a misnomer and wouldn't represent a step forward with regards to the Electoral College system.