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If all you care about is having a chip that implements the
functionality you have implemented at the Verilog/VHDL level, and you
don't care about area, power, performance, then an FPGA is a good way
to go. This is why they are widely used for rapid prototyping.

However, if you care about area/power/performance, custom layout is
the way to go. The drawback with custom layout is that it usually
takes more time/effort/money to do well. But when done right, the chip
will normally be a lot better than an FPGA on all those metrics. Also,
If you're planning on designing a chip that will have high volume,
then custom layout can also be cheaper...

-Rajit

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