The varieties you see in a supermarket are optimized for industrial farming and yes, transportation is one of the things they optimize for. The tomato specifically, though, lost most of it's flavor purely for aesthetic reasons [1]. Consumers have an image of the perfectly round red tomato so all the farmers optimized for it, losing at least one critical gene that contributed significantly to flavor and sugar production.
Those varieties have mostly out competed everything else in farmers markets and supermarkets but if you buy seeds online from specialized stores and grow them yourself, you can unlock an entire universe of flavor. Personally, I've never found a supermarket fruit or vegetable that tastes as good as the ones I have grown or eaten in countries with less industrialized farming, with the exception of designer varieties like cotton candy grapes, cosmic crisp apples, or sumo mandarins (though their quality is rapidly falling as they go from coddled breeding labs to industrial scale). I don't think I've had a "proper" strawberry, blueberry, or raspberry since I moved to the United States.
Depends where you live, but heirloom tomatoes and such are very popular at farmers markets up here, and available at the better stores. (example image from a quick google: https://i1.wp.com/www.seedtopantry.com/wp-content/uploads/20... ) Berry season up here is awesome too even in the major markets, because there's such a glut of berries that won't transport out of the region.
I suspect this will be more of a trend across the US. Every time I visit back home in KS I see more people at the farmer's market there, more stuff in the supermarkets that's trying to regain some farm to table authenticity.
As long as you're grocery shopping in the United States, it doesn't really matter. I've spent most of my life in suburban and exurban California with several years each in New York, Miami, and Seattle so I'm no stranger to farmers markets and co-ops. The difference between homegrown and farmers market is much greater than the difference between farmers market and supermarket.
If I had to quantify it, I'd wager that fruits and vegetables from farmers markets are from 10% to 20% better than what you'd find in a supermarket. Co-ops can be as much as 10-50% better but growing it yourself with proper varieties is easily 200-300% better, especially here in California. Tomatoes with so much flavor that you can taste them through a tablespoon of ranch dressing (not that you'd ever need anything more than a splash of olive oil and a dash of salt with home grown vegetables).
I've also come across an article in a Swiss newspaper according to which supermarkets prefer tomatoes varieties that have a "consistent" taste all year round – and because you obviously don't get extraordinarily tasting tomatoes in winter, this then means mediocre-tasting tomatoes all year round instead.
(So are they afraid that if they start selling truly delicious tomatoes in summer, they will no longer be able to sell mediocre tomatoes in winter?)
Those varieties have mostly out competed everything else in farmers markets and supermarkets but if you buy seeds online from specialized stores and grow them yourself, you can unlock an entire universe of flavor. Personally, I've never found a supermarket fruit or vegetable that tastes as good as the ones I have grown or eaten in countries with less industrialized farming, with the exception of designer varieties like cotton candy grapes, cosmic crisp apples, or sumo mandarins (though their quality is rapidly falling as they go from coddled breeding labs to industrial scale). I don't think I've had a "proper" strawberry, blueberry, or raspberry since I moved to the United States.
[1] https://science.sciencemag.org/content/336/6089/1711.full