Leonardo Da Vinci is usually thought of first and foremost as an artist but he was also an important humanist, scientist, and naturalist in the Renaissance. There is no evidence that Leonardo Da Vinci was also an atheist, but he should be a role model for us all in how to approach scientific and artistic problems from a naturalistic, skeptical perspective. He is also a reason why atheists should pay more attention to the connections between art and philosophy or ideology.
Leonardo believed that a good artist must also be a good scientist in order to best understand and describe nature. The humanistic, naturalistic, and scientific aspects of Leonardo's life and work are not always clear because he was an original Renaissance Man: Leonardo's art, scientific investigations, technological inventiveness, and humanistic philosophy were all bound together.
 

Leonardo Da Vinci's Life & Work

Leonardo Da Vinci was born in the village of Vinci in Tuscany, Italy, on April 15, 1452. His skill and ability to elicit so much emotion with a few simple lines is almost unparalleled in the history of art. While people may realize that he as an important artist, though, they don't generally realize how important he was as an early skeptic, naturalist, materialist, and scientist.
Major eras in Leonardo's Life:

• Florence (1467-1482)
• Milan (1482-1499)
• Italy and France (1499-1519)
• Leonardo Da Vinci died on May 2, 1519, in Cloux, France

Some of Leonardo Da Vinci's surviving works include:

• Annunciation, 1475-1480
• Adoration of the Magi, 1481
• Last Supper, 1498
• Mona Lisa or La Gioconda, 1503-1505
• The Virgin and Child with St. Anne, 1510
• St. John the Baptist, 1514

As with other Renaissance artists, Leoanrdo Da Vinci's works were primarily religious. This is only to be expected since the Catholic Church was the largest, richest institution of its age. It commissioned the most art and architecture, so any talented artist would be working primarily in a religious context. Not all religious art conveys the same messages, though, and not all religious art is solely religious.

The art of Renaissance artists like Leonardo is not the same as medieval religious art. Leonardo placed an emphasis on the humanity of human beings, using Christian types and mythology to convey secular, humanist ideas. The Christianity cannot be separated from his work, but neither can the humanism.

Leonardo Da Vinci's Science & Naturalism

The origins of science can be traced back millennia, but it can be argued that the origins of modern science are in the Renaissance. Two features of the Renaissance factor heavily in modern science: the revolt against religious and political restrictions on knowledge and the return to ancient Greek philosophy — which included empirical, scientific investigation of nature. Renaissance figures like Leonardo Da Vinci were explicit in their reliance on empiricism rather than faith, their willingness to study nature to gain knowledge rather than rely upon tradition or dogma.
Leonardo Da Vinci exemplified this attitude through his careful studies of the natural world. He didn't just wonder how birds flew, for example, he undertook systematic studies birds in flight — then took this knowledge and tried to apply it in the hopes that humans might fly as well. Leonardo also studied how the eye sees in order to apply this knowledge to improve his own artistic creations.
Guided by the conviction that nature always takes the shortest path, he developed early theorems of inertia, action/reaction, and force. None was as developed as those made famous by Descartes and Newton, but they demonstrate his involvement with science as well as the degree to which he placed empirical data and science above faith and revelation. This was why Leonardo was such a strong skeptic, casting doubt on popular pseudosciences of his day - especially astrology, for example.
 

Leonardo Da Vinci & Renaissance Humanism

As one of the central figures of Renaissance Humanism, a central focus of all Leonardo Da Vinci's art and science was the human being. A focus on human concerns rather than otherworldly concerns lead Renaissance figures like Leonardo to spend more time on work that would benefit people in their daily lives rather than the otherworldly interests of the Church.
The Renaissance focus on humanity was an outgrowth of the interest in Greek and Roman philosophy, literature, and historiography, all of which offered a stark contrast to what had been produced under the direction of the Medieval Christian Church. Renaissance Italians felt themselves to be the inheritors of Roman culture — an inheritance which they were determined to study and understand. Of course, study led to admiration and imitation.
We have no direct evidence of Leonardo Da Vinci himself being obsessed with or trying to imitate ancient Roman culture, but key in Renaissance Humanism for us today is more its spirit than its content. We have to contrast Humanism with the medieval piety and scholasticism against which Humanism was regarded as a breath of fresh air. Renaissance Humanism was a revolt — sometimes explicit, sometimes implicit — against the other-worldliness of medieval Christianity. Humanists turned away from a religious preoccupation with personal immorality, focusing instead on how to enjoy, make the most of, and improve this life for the humans living it.
Renaissance humanists didn't just write about new ideas, they lived their ideas as well. The medieval ideal was the ascetic monk, but the Renaissance gave us the ideal of the Renaissance Man: a person who lives in the world and learns as much as they can about as many different features of the world as possible not just for the sake of esoteric knowledge, but to better improve human life in the here and now.
The anti-clerical and anti-church inclinations of the humanists were a direct result of their reading ancient authors who didn’t care about gods, didn’t believe in any gods, or believed in gods who were far and remote from anything that the humanists were familiar with. Renaissance Humanism was a revolution in thinking and feeling which left no part of society, not even the highest levels of Christianity, untouched.