Hi Luka,
The filter wizard circuit does not do any level shifting. It assumes the input signal and output signal will be centered around the same reference voltage. So in your example, it assumes the input signal will be centered around 5V. It will not work if the input signal is centered around 0V.
The Analog Dialogue article first applies a passive high filter to the signal before it reaches the op amp circuitry. This allows you to send in a signal centered around any voltage you would like, including ground.
You could add one of the stages shown in the article before the circuitry the filter wizard generates. This should work. However you will now have a high pass (generated by Analog Dialogue circuit) followed by a low pass (generated by the filter wizard software.) In other words a bandpass circuit.
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I wrote the above assuming your input signal is biased around ground and this is why the circuit does not work. If your input signal is centered around 5V and your circuit is still not working, can you give more details?
Thanks,
Matt