If you planted multiple tomato seeds in each cell and more than one has germinated, yes, you can safely separate them and transplant each one into its own new pot.
If you transplant seedlings on a hot sunny day, the heat and the sun could cause them to go into shock. Waiting for a series of overcast days to transplant them is best.
At planting time, you will want to bury as much stem as possible, as the tomatoes will grow new roots along the lower stem, which makes for a stronger, healthier plant.