Surprised no-one has mentioned this yet, but another problem with Flash is its limited number of re-writes.
For a FPGA in a relatively static application (like in most consumer electronics?) this wouldn't be an issue. But there are surely FPGA uses where the FPGA is re-configured (differently!) many times, say some high-performance computing or scientific applications. Integrated Flash might wear out in such uses, and then the FPGA becomes defect / useless.
Probably not the reason for Flash based vs. SRAM-based market %, but possibly a reason contributing to what others already said.
Although this is a bit late, this post makes a point a few others have noticed. The technology, SRAM or Flash, is utterly irrelevent to the speed of the array but does have an impact on Iq as RAM does need a bit more power than Flash. The reason is the flash cell is either on or off, but is only 1 transistor whereas RAM is several transistors (it take at least 6 to make a really low power RAM cell as these cells are static RAM). The reason this is irrelevent to the array is that these cells control a T gate or a MUX and have no other interaction with the logic. The memory is
static. Only fuse based arrays are faster and these are not reprogrammable. The popularity of RAM based cells is based on maturity of technology and process (it's cheaper to make because it's what they started with) and has no reprogrammability limits. FerroRAM cells, which are Flash cells with a different gate insulator material that offers infinite reprogrammability, may replace both RAM and Flash in the future.
RAM based: Larger arrays with smaller and (sometimes) faster logic elements, infinite reprogrammability, ubiquity (almost any maker of RAM based FPGAs can be replaced by another, if not pin for pin), faster reprogrammabilty and cheaper.
Flash Based: Lower power, non-volatile and fewer parts.
Fuse Based: Lowest power, faster, higher density, but not reprogrammable.