It's very hard to go into why a legacy played out the way it did, but maybe I can give you a few possibilities.

There is obviously the question of when the policies and programs began to really have an effect on the US economy, and when the US economy got better. It's easy to say that foundations were laid down, and another thing entirely to say things got better under the program. In this, the minds of people alive at the time likely would've associated economic rebirth of a sorts to FDR, not to Hoover.

Another one of the main problems is that Hoover actively spoke out against the New Deal throughout 1934-1936. He wrote a friend in the weeks after he lost his attempt at re-election, that:

When the American people realize some ten years hence it was on November 8, 1932, that they surrendered the freedom of mind and spirit for which their ancestors had fought and agonized for over 300 years, they will, I hope, recollect that I at least tried to save them.

This was only the beginning of his anti-New Deal rhetoric. Hoover would write in a letter that Republicans should assert that the depression was born of war, that recovery was won in the summer of 1932, and that Roosevelt set it back. He also equated the New Deal to socialism and fascism (or said it would lead there, at least), and spoke out publicly against it in 1935, giving at least one major speech a month on average until the Republican convention of 1936, since he was trying to get the nomination to run again (he was never really considered a serious candidate, though). Speaking in St. Louis, he said:

We have executive orders, propaganda, and threats substituted for specific laws. We have seen the color of despotism in the creation of a huge bureaucracy. We have seen the color of Fascism in the attempt to impose government directed monopolies. We have seen the color of Socialism by government in business competition with citizens.

As you can imagine, this type of rhetoric doesn't help him gain points for any New Deal-esque policies he may have implemented.

Hoover also lacked many of the qualities that made FDR so memorable, and which helped him win so many elections. People would lament his speeches, calling them boring and laden with statistics, which didn't help him become a memorable figure. While that changed after 1932 when he began lambasting the New Deal (leading to him being called "New Hoover" by some pundits), it wasn't enough to change the overall perception of him (especially since he hadn't yet really learned to use radio to his advantage before 1932).

Also, Hoover's strategy was far more focused on belt-tightening and reduced expectations than the more radical New Deal policies. Hoover would say things about how the depression could not be cured by "legislative action or executive pronouncement. Economic wounds must be healed by the action of the cells of the economic body--the producers and consumers themselves." He refused, in many cases, to get the federal government involved in direct relief for individuals. While in many ways he did encourage it, part of his problem was that he was not forceful in the presidential role as chief legislator (in the sense that the Constitution provides for the president to recommend and push legislation the president finds necessary and expedient). He appealed far more to the private sector to lift the country out of the Depression than to the government. He was a very different person than FDR, and was greatly overshadowed by him. So while Hoover may deserve some small modicum of recognition for his work, it was poorly pushed, his overall policy was one of constitutional restraint preventing more action, and he was, compared to FDR, a boring figure. He placed more faith than FDR in individualism and the good of people, while FDR preferred direct government intervention to a much greater degree, so while he laid the groundwork it was hard to remember his legacy when it was overshadowed by the more forceful and popular FDR.

Hopefully that helps!

Sources:

The Rhetoric of the Post-Presidency: Herbert Hoover's Campaign against the New Deal, 1934-1936 Brant Short Presidential Studies Quarterly, Vol. 21, No. 2, Measures of the Presidents: Hoover to Bush (Spring, 1991), pp. 333-350

The Politics of Less: The Trials of Herbert Hoover and Jimmy Carter David D. Lee Presidential Studies Quarterly, Vol. 13, No. 2, The Institutional Presidency (Spring, 1983), pp. 305-312