Since their first appearance in Fantastic Four #2 (by Stan Lee and Jack Kirby) the shapeshifting alien race known as the Skrulls has always been a thorn in Earth's side. Though they hailed from a regal cosmic empire, they were also embroiled in serious conflicts, most famously with the Kree Empire. As a result, they were just as skilled in combat as they were in science and deception. Their unrelenting war also drove them into a secret invasion that nearly decimated the Skrull race.
Secret Invasion (by Brian Michael Bendis, Leinil Francis Yu, Mark Morales, Laura Martin, and Chris Eliopoulos) followed the Skrull Empire's deadly invasion of Earth after they spent years infiltrating the human race. By replacing heroes and people in power with Skrulls, they tried to take over the planet and make Earth their new home. However, when Norman Osborn killed their queen, it was clear that, while the Skrulls were antagonists, they were victims, too.
Skrulls Were Forced To Invade Earth
Skrullos was the Skrull Empire's homeworld and the species took great pride in it. However, they lost Skrullos in their ongoing war against the Kree Empire. This loss devastated the Skrulls and turned the once-proud empire into a collection of galactic refugees. Now in need of a habitable planet, this loss forced the Earth into the Skrull's sights and started a systematic invasion that was brought to light when Elektra was revealed as a Skrull in New Avengers #31 (by Brian Michael Bendis, Leinil Francis Yu, Dave McCraig, Richard Starkings and Comicraft's Albert Deschesne).
Tragedy forced the Skrull Empire's hand because they were backed into a corner. Their quarrel was never with Earth, but the planet became not just a part of their war, but a key for their survival. After their failure in Secret Invasion #8, Hulking, a half-Skrull/half-Kree hybrid, commented on how this behavior was uncharacteristic of the Skrull Empire. This compounded their tragedy because they still had no home and they'd turned Earth's heroes into a lethal enemy.
Skrulls Had No Larger Conflict With Humans
Before Secret Invasion, some Skrulls had attacked Earth. The most famous example of this was the constant battles between the Super-Skrull and The Fantastic Four. However, even though the Skrull Empire had its misgivings about the FF, Earth and the Skrulls shared a tense but otherwise peaceful relationship. The Skrull Empire had always been at war with the Kree and, as a result, never took on another larger battle. This is why they chose to secretly invade Earth. They had no way to fight two large-scale wars.
Aside from when the Skrulls faced Earth during their conflict with the Kree in The Avengers: Kree/Skrull War (by Roy Thomas, Neal Adams and Sal and John Buscema) the Skrulls weren't in conflict with humanity. In the end, it's clear that the Skrulls were already in dire straights and were desperately trying not to die. The Secret Invasion was their choice but now caught between Earth and the Kree Empire, they were its victims in more than one way.