Sorry to hear. It is possible that the roots were in air pockets or damaged to where they could not get nutrients, but tomatoes when repotted and buried 2/3 of the plant will usually form roots on the stem when exposed to the soil. The cotyledons should provide them enough oomph to get established. It might be something else.
This isn't the solution to your current problem and since they didn't survive it isn't applicable, but rather some growing tips to increase the survival rate and health of tomatoes for other readers.
I have two growing seasons where I live and for the first season I try to get them started early before the sweltering heat and hungry insects eat the fruits of my labor.
Determining When to Sow Seeds
Determine the last frost date in your area and work backwards. Subtract 1 week for germination, then 4-6 weeks which is usually the age they use for the Days to Maturity. That should be your sowing date. If it is cold at time then you can start them inside under a heating pad on low power to warm the soil since they are tropical in nature. Also be mindful of the days to maturity in case you have a shorter growing season. Some varieties like Azoychka have a shorter days to maturity than the larger beefsteak varieties.
I do it via wet paper towels in a small plastic sandwich bag, but you can do it in a tray with a small amount of potting mix with a clear tray cover for a greenhouse. When they sprout you gently transplant them to your pots. I use a sterile potting medium and bury them 1/2 to 2/3 of the plant height deep. I repot as necessary staying away from the peat pots. Always bury them 2/3 deep for stronger root structure. I keep the soil warm to trigger plant growth otherwise they slow down so I keep them inside and/or keep them under the heating pad at night on low to keep the soil warm.
Light from a southern window isn't enough for tomatoes and also your glass my have UV coating. Even if you have the window open they may not be getting hours of daylight they need. I setup a fluorescent shop light and put the tomatoes under them. They aren't hot so keep them within 1 inch(2.5cm) of the top of the plants day and night so that they will get as much light as possible. Sunlight is preferable, but at night you should still give them light as well. For me it is easier just to keep them under shop lights.
As the Tomato plants grow upwards toward the light move the light so that the top of the plants remain within the 1 inch (2.5cm) spacing. You can also put a small fan about 3 yards (1 meter) away from them on low power for a few hours. This wind will activate hormones in the plant so that it won't be spindly/leggy and a more stockier plant. You can do the same thing by gently moving your hand over the top of the plants daily.
I alternate waterings with feedings every other week with a diluted fish emulsion or kelp at 1/4 to 1/2 the recommended rate. I have the pots in a tray and water from the bottom to reduce the chance wetting the leaves. If you prefer to use synthetic liquid fertilizer you will need to figure out the ratio, but start at the low end ratio like 1/4 ratio to reduce the chances of burning the plant.
After the 3rd or 4th week I may repot if they are getting root bound. If you use clear plastic cup or the hydroponic basket style pots where the soil is visible you can montitor the roots. Again, for every transplant try to bury the plant in the new pot at 2/3 depth (remove bottom leaves if needed) so that the plant can have a good root system.
When the weather forecast calls for a mild or warm temperature slowly harden them off by taking them outside gradually (an hour at first then longer periods) and increase the outside time until they are about 5-6 weeks old. Eventually have them out overnight in a place free from pests/animals. This will reduce the amount of transplant shock when you do put them in your garden.
I tend to have more plants than garden planting space so I pick the best plants and give the remainder to my family and friends. Again make the planting hole at a depth that is 2/3 the height of your plant and remove bottom leaves/suckers if they are below the soil. You can put a handful of crushed eggshells mixed with bottom soil. It is better if you grind them in a blender or coffee grinder so that they are dust rather than shells. This will make them more readily available. I put a handful of vermicompost in hole as well. I put a top dressing of compost with about 4-5 inches (10-12 cm) of mulch. Water well.
Remove any flowers to encourage plant growth. Keep the soil well fed and alive with amendments and organic material.