The subjunctive is no longer used with that construction unless it is a question, in which case it becomes optional:
- ¿Crees que vaya a llover? / ¿Crees que va a llover = Do you think it is going to rain?
If the sentence is negative, the use of the subjunctive is mandatory:
- ¿No crees que vaya a llover?
According that site the following constructions don't trigger the subjunctive
Creer que. This uses the subjunctive if it's used in a question.
No dudar que. This uses the subjunctive most of the times, but it's optional.
Estar seguro que. This is a very common mistake (queísmo), the correct construction is estar seguro de que.
No es dudoso que. As far as I know, this is always used with the subjunctive.
No hay duda que. I'm not sure what they meant by using this construction, but whether it is no hay duda que or no hay duda de que, both would use the subjunctive, but it would be optional with the second one.