(prepare yourself for a horrible analogy)
Think of space as the ocean and the field lines as fish. Now, imagine there is one part of the ocean that has an abnormally large number of fish. Also, these fish come in many different lengths. Now say you're a fisherman and you want to catch some fish. Your salary, however, is dependent on the length of the fish you get, i.e. the longer the fish, the more money for which you can sell the fish. There's also another catch. The longer fish are a lot stronger and faster than the smaller ones, and so you can only allow so many to pass into your low-tech circular net at the same time or else your net will break or the fish will force the net out of your hand.
So now you have some calculating to do. You don't want to lose or break your net, but at the same time, you want to get as much as possible. Therefore, you must consider two things - the size of your net and the size/strength of the fish you're going to catch. If you're in an area of really small fish, you want to use a larger net. If you're in an area with large fish, you want to use a slightly smaller but stronger net.
Think about this relationship between netsize and fish size. You can sort of picture an inverse proportion between them. Think of flux as the proportionality constant between this relationship. It's the product of the opening size of your net and the strength/size of the fish. Alternatively, you can think of flux as the amount of money you'd make, since, in my made-up world, selling the large net's worth of small fish gets you the same amount of money as the small net's worth of large fish.
Now (the tricky part), try to apply this situation to electromagnetism. As you said, there are, theoretically, an infinite number of field lines. This is because it is assumed that these field lines affect all of space and therefore should exist everywhere. However, the strength of these field lines is not the same everywhere (This is the part that you have to convince yourself). Recall that the electric field of a point charge decreases by 1/(r^2). Flux is always calculated, as previous posters have said, as the product of the surface area and the perpendicular field that penetrates that surfaces. Think of the surface as the 'size of the net' and think of the perpendicular field as the fish that are swiming directly into the net.
Now, say you are trying to find the induced current on a loop of wire. It turns out that it is proportional to the magnetic flux through that loop. Think of the magnetic field as being the 'fish' and the loop of wire being the 'net.' To find the magnetic flux, you need the amound of field passing through the loop.
I hope that helps, though I completely understand if it doesn't.