Short answer:
Negative thoughts in Cognitive Behavioral Therapy are both a cause and a consequence in depression. In fact if these thoughts are produced by schemes this theory considers as a specific factor of vulnerability that predisposes to depression in certain events.
Long answer:
First of all we should consider the considerations in terms of schemes in depression, there are different theories in depression that address schemes:
Behavioral Cognitive Therapy.
Emotion-Focused Therapy.
Emotional Schema Therapy.
Mindfulness to avoid recurrence in depression.
All these therapies consider schemas in a central way and there are important subtleties in the consideration of such schemes.
The fundamental thing in Behavioral Cognitive Therapy is that the processing from these schemes is a key factor in the maintenance of depression. Also the Focused Therapy in Emotions considers dysfunctional schemes in the maintenance of the depression however, although it considers them necessary, it does not consider them sufficient.
Document with some contents about schemes in Emotion-Focused Therapy:
https://www.researchgate.net/publication/307869346_Affective_Change_in_Psychodynamic_Psychotherapy_Theoretical_Models_and_Clinical_Approaches_to_Changing_Emotions
Document with some information about schemes in Emotional Schema Therapy:
http://www.thrivetraining.info/wp-content/uploads/CPI-18-A-Model-of-Emotional-Schemas.pdf
Document that you cite, prepared in 1981:
http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.380.5119&rep=rep1&type=pdf
Later, Peter Lewinsohn formulated his theory of depression (Lewinsohn, Hoberman, Teri and Hautzinger, 1985).
Lewisohn postulates that environmental factors are primarily responsible for depression, although there would be cognitive mediating factors. The main mediating variable is the increase of self-consciousness, transient and situational state of self-focusing or amount of attention that a person directs towards himself instead of towards the environment.