So this comes up often enough that the Army actually has its own FAQ answer about it here! https://history.army.mil/html/faq/base_name.html

It boils down to for about 50 years the Army would be perfectly willing to bow to local pressure if it meant those regional interests would support the base.

For much of the Army's history in the 19th Century, the naming of posts was still mainly a local prerogative. For example, War Department General Order Number 79, dated 8 November 1878, left the naming of installations to the commander of the regional Military Division in which the installation was located. Although not always, the names of installations usually reflected a local influence, such as Fort Apache in Arizona, established in 1871, and the Chickamauga Post in Georgia, established in 1902. In the 1890s, the then Quartermaster General, Maj. Gen. Richard N. Batchelder, recommended that the War Department assume responsibility for naming installations, but that did not become policy until World War I when the massive general mobilization saw the establishment of numerous installations of various sizes and functions. The names usually, but not always, reflected some regional connection to its location, and usually with a historic military figure significant to the area: for example, Camp Lee near Richmond, Virginia, and changing the name of the Chickamauga Post in Georgia to Fort Oglethorpe.

In the years between the World Wars, it became the common practice for the War Department to entertain recommended names for posts from installation commanders, corps and branch commanders, and the Historical Section Army War College, as well as from outside the Army. Public opinion and political Influence sometime weighed heavily on the decisions. For an example of the latter, when in 1928 the Army renamed Fort George G. Meade in Maryland as Fort Leonard Wood, the Pennsylvania delegation in Congress held up the Army's appropriation bill until the service agreed to restore the name of the Pennsylvania-born general. The regional connection, however, cannot be overemphasized. Fort Monmouth in New Jersey, for example, was originally named Camp Alfred Vail, in honor of the Army's then chief Signal Officer, when the installation was established as a Signal Corps training facility in 1917, but changed to Fort Monmouth, for the 1778 battle fought nearby, when it became a permanent installation in the 1920s.

Emphasis mine

Hence why Forts Lee and AP Hill are in Virginia, Fort Polk is in Louisiana, Fort Bragg in North Carolina, Fort Benning in Georgia, and so on. Though sometimes the connection is as tenuous as a nearby birthplace if that. And we should recall that many of these forts and camps having been founded at the height of the Lost Cause which glorified most CSA leaders as noble men fighting for their states rights, and minimized many of the issues which would to a modern audience made the naming of them more problematic, namely most racial aspects of the war and the Southern cause.

Additionally with much of the Army itself more interested as a policy matter in a reunited nation, and enthusiastic mobilization in war time over ensuring the goals of racial equality or social reform were met, names of bases founded in a hurry to support huge numbers of draftees like Fort Lee were easy to let local communities(well the white communities at least by and large) feel ownership of them. While many were held in some level of esteem and respect from their battlefield exploits.

While as a final note it is far from the only time the US Army has elected to name things after defeated, esteemed foes, despite any problematic appearances. Notably helicopters are named in pattern after Indian tribes which almost one and all were in conflict with the US at some point during westward expansion. The Iroquois, Chinook, Lakota, Blackhawk, and Apache all have had their turn in this as examples.