Assuming you are referring to the coups of the post-WWII period, and not the early 20th century, the answer is mostly that the US participated and supported these coups, but they did not unilaterally overthrow governments. In every case where the US supported the overthrow of a government they didn't like, it was through backing local actors who already wanted to overthrow the government. . Even if it were possible to simply "replace" a government with a liberal democracy, which is an idea with a fairly dubious track record, the US simply wasn't very interested in that outcome. The actors they supported in these coups were very seldom democratically minded. Instead, they were usually right-wing forces, generally emerging out of the military, who saw themselves as doing what was necessary to save their countries from the popular madness of left-wing rule. Regardless of what choice the State Department might have made in a vacuum, the reality on the ground was simple and brutal: if the military seizes power in a coup d'etat, and remains in control, then the resulting government is almost by definition a military dictatorship.
(Note: Fascism is more an epithet than an accurate description here; right-wing military rule in Latin America doesn't share common origins with actual 1930s Fascism, which as a model is more influential for Getulio Vargas or Juan Peron than the more straightforward right wing dictatorships of Pinochet or Videla.)
As for why the US pursued this policy line, the answer is a bit complicated, because the US is a complicated beast. But mostly, it's a combination of "because we can" and "communism." The United States has a history especially in the Caribbean of using blunt force to get what they wanted. Overthrowing governments they found inconvenient was well within their capacity, and so they did - who was going to stop the United States, the global superpower, from doing what it wanted so close to its own borders? The other reason was opposition to the Soviet Union, and to communism and socialistic ideologies more generally. Ideological posturing acted mostly as a fig leaf for rampant interventionism early on, as in their support for Somoza against Sandino in Nicaragua in the early 1930s, or the overthrow of Arbenz in Guatemala in 1954. There were many-pronged efforts to secure US influence in the region, including the infamous School of the Americas, which brought members of Latin American militaries to train in the US, and ensure that they remained friendly to US interests and hostile to communism.
But after the Cuban revolution in 1959, the US started taking Latin America a lot more seriously. The region was seen as fertile ground for homegrown communism, and took decisive steps to prevent any further successful communist revolutions, which would lead to embarrassing and strategically awkward hostile states deep within "their" sphere of influence. And so, the priority for American policy vis a vis Latin American states was to prevent domestically-grown socialist movements from taking power and orienting their countries away from the United States' influence.
There were attempts at doing this peacefully via aid and support, including the Alliance for Progress, the Inter-American Development Bank, and so forth. But this was trying to put out a forest fire with a squirt gun, and failed to solve the deep political and economic problems that drove popular support for left-wing governments. If those governments were popularly elected and unlikely to be ousted at the ballot box, then a military coup was the obvious alternative. The economic slowdown and crisis of many Latin American countries in the 1960s and 1970s gave ample excuse for a crisis that would justify takeover. In each case, domestic actors were the prime movers, right-wing factions within the countries themselves looking to take power and change the ideological direction. But the US was nevertheless instrumental in providing support and coordination for these regimes, and of course they were recognised rather than made into pariahs by US diplomacy.
By the late 1980s, the cold war was winding down, and the military regimes had largely imploded under the combined weight of the perennial economic problems of Latin America, and their own colossal incompetence. The US largely stopped its support for right-wing dictatorship, and left the region to re-democratise. The counter-example of Venezuela is notable for being closer to the older pattern of intervention, but is also outside the scope of this subreddit.
/u/ainrialai has given this topic a great deal of thought. From her(?) greatest hits:
/u/PotatoPactSignatory and /u/ColloquialAnachron have previously written about US civilian public awareness of the coups d'etat in Iran and Guatemala. ColloquialAnachron has also answered What were Eisenhower's reasons to overthrow Arbenz in Guatemala? I've run out of pings so I will add more shortly.
EDIT: forgot hyperlink for Arbenz question.
EDIT2: See below for an answer about the Monroe doctrine, important background for why the US felt compelled/entitled to intervene.