We have Flea Markets here too.
The difference between the 2 is that at a Car Boot Sale your stall is the boot(/trunk) of the car.
The difference is most "flea" markets are held in town on the market stalls as for regular markets, and generally if you sell at more than 1 or 2 weeks of these in town markets, you have to become a member of the market traders federation and the associated membership fees and really are classed as a "Sole" Trader as a business and subject to the rules/tax/income etc around that.
Car Boot Sales are outside these rules and as such a regular seller isn't bound to be a business and not subject to those rules/tax/income etc.
Basically if you want to keep the states fingers off your profits, Car Boot sales is the "Dark/Black Market" whereas Flea markets are were the "dealers" hang out. Although they also do the car boots too.
I was a flea market seller for around two years, I got round the rules by having different people standing and rotating between about 10-15 markets, problem was my "turf" suffered from living around an Antiques trade area where the prices went through the roof in the summer months, due to tourists and I couldn't be arsed standing week in week out during the winter. One thing I take my hat off to are those that do markets 365, hardier souls than me. Went back to an office job and haven't looked back.