The present x86 isn’t made from the ‘same process and materials’ as the 6502, any more than a modern automobile and a Model T are.

But your point is taken that they’re both based on silicon. Nevertheless, decades of continuous development and innovation have steadily improved the performance of silicon process.

The biggest improvement? Channel length (feature size generally) makes a huge difference in CPU performance. Contemporary CPUs have channel lengths about 1000x shorter than the 6502:

 * 6502: 8um
 * Typical CMOS today: 7nm

This key difference affects gate delays, which ultimately determine the achievable cycle time. Smaller features also reduce capacitance and wire delays, further boosting speed.

Also note that the 6502 was an NMOS part (CMOS ones came later) which also puts it at a disadvantage over contemporary CPUs. But really, it’s the smaller feature size that makes the difference.