The whole population of each of those places doesn't benefit, just those who use the trains and or benefit indirectly through the multiplier effect. It is not the whole population or anything close to it. And some will benefit more than others.
Meanwhile on the A303, every single person who uses it (and I think there is something like 40,000 vehicles every day past Stonehenge) will benefit to the tune of quicker journeys and lower fuel consumption. Speaking very personally, I never consider going to Devon or Cornwall for a holiday as the traffic is so bad en route, with Stonehenge at #1 on that list. With that sorted I may well reconsider.
I would be willing to bet that if you surveyed the population of Exeter, Plymouth, Crediton, Okehampton and Launceston what they would rather have; an improved A303 or a second rail route from Plymouth to Exeter, a very significant majority would pick the former. You'll be hard pressed to find someone in Devon who hasn't been stuck in A303 traffic.
For Crediton, Okehampton, Tavistock and Launceston, you're not just talking about "a second rail route from Plymouth to Exeter" you're talking about their local railway route. A majority might prefer the road improvement, however, a significant proportion would probably prefer decent public transport (perhaps even in proportion to the relative cost the two projects).
Not everybody in Devon and Cornwall and Devon will travel down the A303 either.
] I commuted from my home near Tavistock to my workplace near Aldershot on a weekly basis, using a mixture of car and train -indeed I did get stuck in A303 traffic on quite a few occasions, although generally it wasn't really that bad. But had the option of travelling directly by train from Tavistock been available, then there is no way that driving would have been even a semi regular choice and it would be no different even with an improved A303.The Tavistock to Okehampton road is not exactly a racing track and the thought of getting on a train, being able to relax, do a bit of work or whatever would have been a no brainer option and, although I agree that the great majority of people still use the road in comparison to rail, i would be willing to bet that a very reasonable amount of business would be attained via others in this area who feel the same way as me, no matter where their destination is.