Probably not to a degree that would be any worse than a comparable volume of car or truck traffic passing through the same region on highway. Trains could also pass through it at a much higher rate of speed with fewer overall emissions of pollutants, which further minimizes the impact. In particularly sensitive areas perhaps special types of tracks could be built to protect wildlife. All these problems can be overcome. Replacing caravan after caravan of cargo trucks with relatively less-polluting trains could persuade many environmentalists to sign-on.
Will train travel catch on with the average consumer? That's debateable. The business traveler who has to leave NY and be in LA before the meeting the next morning won't be inclined to take the train. The college students, the tourists, the holiday traveler, and others who don't necessarily have to be there the same day, may opt for the slower (and hopefully cheaper) train. I think where passenger travel by train could REALLY catch on is in the realm of commuter-rail travel.
I live in Colorado Springs and a couple times a year I need to go to Denver International Airport, a mere 85 miles. Driving there is fine in the summer, takes about an hour and a half or so depending on traffic. Driving there in winter time (like Christmas) can be a hair-raising experience. Getting there in a timely fashion (or at all) in winter depends on: whether the freeway over Monument Hill has been plowed, how many cars are in the ditch attended by state patrol causing rubber-necking slow downs, and how fast I can drive before my "all-weather" tires start to wobble like a top about to fall over. I only dare such a trip because I have no other choice.
I'd love to be able to go to the train depot in downtown Colorado Springs, hop on the high-speed rail to DIA, and just relax the whole way. Traveling in a warm quiet cabin, able to browse online, maybe have a nice latte while still getting there in half the time.