First of all, Shiva, Vishnu, and Brahma are worshipped in the Rig, Sama, Yajur, and Atharva Vedas, but it’s true that Indra is far more emphasized.
The way in which I account for this fact is based on my perspective as a traditional Pauranika Hindu. I consider the trinity of Brahma, Vishnu, and Shiva to be of infinitely greater cosmic importance than Indra. However I also consider the Vedas to be the supreme sacred Shruti, whose Sanghita Mantras were heard by the ancient Rishis and Rishikas from the primal sounds of existence itself. I see no contradiction in this, but it does require a certain understanding of context.
So what are the Mantras of the Vedic Sanghitas for? They are certainly not a straightforward explanation of the nature of existence, as is obvious if you read any part of them. They read like mystical poetry, mostly in invocation of various Devas (like Indra).
The Vedas’ Brahmana and Aranyaka chapters say exactly what the Sanghita Mantras are for: they are Mantras to be used in the performance of certain Yagnyas. These Yagnyas have exoteric applications and esoteric applications. The esoteric applications are within the Sadhaka, and are explained in the Upanishad chapters of the Vedas. They deal primarily with the Ultimate Reality, Brahman, and the identity of the Atman or Self with Brahman.
The exoteric applications of Vedic Yagnya deal with the external world: weather, agriculture, the sky and the earth, rivers, etc.: all the practical needs of the Vedic people. The Yagnyas are for influencing those elements of the external world: managing the rains, for instance. As such, they work directly with the Devas, or deities of nature, pertaining to those elements.
So of course Indra is the primary deity of the Vedas: he’s in charge of rain! This is only practical. If your lock is broken, do you pray to God to fix it, or do you hire a locksmith? The Vedas sensibly take the latter approach.
In Kali Yuga these exoteric Yagnyas are difficult to perform correctly, and so they are not currently the efficacious tools to manipulate the natural world that I believe they usually are.
This is the traditional understanding of popular Hinduism.