What is the ruling on working for a software company owned by a person who is among the people of innovation (Ahl al-Bid'ah) and also owns a heretical religious tourism company? Is the money earned from this work subject to the suspicion of being unlawful (haram)?

The general principle is that it is permissible to work for a remuneration for an innovator (mubtadi') or someone who differs in عقيدة (creed), as long as it does not affect one's own عقيدة or prevent one from performing the rituals of their religion. The Prophet, peace and blessings be upon him, and his companions, dealt with Jews.

As for the specific work mentioned, if it is permissible and does not involve assisting in haraam (forbidden acts), then there is no issue with it. However, if it is haraam or involves assisting in haraam, then it is not permissible, based on the Almighty's saying: "And do not cooperate in sin and aggression." If there is any doubt (shubha) about it, then it is better to avoid it.