Technically, it is possible to change the color of anything with CSS. As mentioned, you can't change the background-color or color but you can use CSS filters. For example:
input[type="checkbox"] { /* change "blue" browser chrome to yellow */
filter: invert(100%) hue-rotate(18deg) brightness(1.7);
}
If you are really looking for design control over checkboxes though, your best bet is to do the "hidden" checkbox and style an adjacent element such as a div.