Ooohhh boy. My brothers 99 had/has this exact problem. If you have the flashing light by the clock it is definitely the immobilizer. We have been fighting this for months. Couple of things that were suggested to us: check that you don't have another key win a chip on your key ring. Sometimes this can confuse the system as it reads what is right in front of the key slot.
Make sure you have a master key. There is a way to rest it using some brake pedal/ turn on/off the key in a sequence. Search on mud. Since my brother only had one key, we got another master and reset it through Toyota.
That worked for a while, but not for long. We then replaced the transponder coil and the amplifier that goes with it. Seems to be okay for now, but every now and then, it's acting up again.
The symptom is the same every time: he puts the key in, the red car light flashes, crank, but no start. He can usually try putting it in and out a few times and then the light will go off, but sometimes it's just dead. Very annoying problem. If you find a solution, we would be very grateful to know.
It's maddening because it's a great truck that is otherwise very reliable, the the stupid anti-theft thing will leave you stranded at random and with no hope of repair since it requires a tech stream enabled computer to even try to fix it.
Cheers!