The Democrats had the majority, but the Republican's used the pseudo-filibuster bullshit to prevent any legislation from passing. When they realized that the ACA they let slip through was much bigger for Obama than they expected, after major negotiations neutering it and in-fact supporting the individual mandate as a compromise, they panicked and since then just "filibuster" instead of trying to negotiate on everything. (Saying your negotiating and compromising when its 'my way or the highway' every fucking time even after concessions are made by Democrats on the various legislation pieces does not actually equal negotiating and compromising).
The Dems had majority, but the Reps used the loopholes to command the power like they were the majority. That's why people can be confused about it.