There's multiple differences which aren't always clear with Low Cost Carriers. Best to try and quantify.
1) They are not always very low fares, low cost does not mean that. Flybe, Jet2 and Wizzair often have the regionals locked up so a Budapest from BHX or MAN is pretty much the price of BA via LHR. Ryanair can be very low fare, like £15 to Glasgow at short notice, so are more likely to be low fares.
2) The lowest fares, if they have them, are leaving early in the morning (pre public transport, so drive and parking, taxi or hotel overnight) and arriving late at night/early in the morning. However, you'll see the same thing with BA at Gatwick for their lowest fares, just not the same level of lowest fares.
3) Only Ryanair really does the fake airport thing. The rest at least seem to aim for the right airport. Bear that in mind, of course.
4) Hold luggage being paid for doesn't mean its a great service. They rarely man the desks with many people (and usually airport staff in remote airports), and don't open checkout until two hours out. So you can easily spend an hour checking your bag in because of the queue. The remote end and pickup is no better, often you're the last one processed having paid the least for the baggage handlers and don't be surprised if it passes an hour before your bags arrive. This seems to be across a few low cost carriers, and it gets worse late at night too.
5) Sometimes the food is actually nice, because you've paid for it. The ploughmans on flybe for instance is quite excellent.
6) They often enforce priority boarding and seat assignment because they are paid. Ryanair has recently been accused of deliberately seating unreserved seats badly, like in middle seat. A recent flight with them had really quite high prices for even normal seating reservations, £4 for an aisle seat at the back, I paid £6 for aisle seat middle of the plane. Easyjet got me one near the front for £4, wizzair would charge £2-3 for near the front. But once you're in, you might well not be allowed to move. You've paid the cheapest price and I think this is where the likes of Ryanair really show that a decent flight involves something more than the basic dare.