I agree with BCK, as long as it is kept clean, you will be AOK.
I would also, if worried aboug fungi and mold, microwave or boil the water... (microwave is probably better... nothing kills like cosmic rays right!?
)
but yes, as long as it is kept clean, and you make sure your not watering with dust and other particulates, I would say your doing A OK, and you could always run it through a paper coffee filter to get the larger matter as well..
but one thing is certain, unless you have a lot of mineral dust floating around your house (live near a rock quarrey or something) your getting a very clean form of water.
Just keep the de-humidifier clean.