The shortest answer: preference.
The short answer: time preference and a preference for risking the punishment.
The longer answer...
If you accept that the 3% deficit limit can be generalized and France is not alone in having a deficit most years, then the question is similar to one that asks: why do countries sometimes have deficits?
The budget balance is determined by factors such as the time preference (the perceived value of current government spending and the perceived value of deferred or future government spending) and the ability to raise taxes without decreasing productive activity and the anticipated future government income stream. The birth rate, immigration, longevity, the retirement age, and productivity improvements would be some of the factors affecting future government income.
If you think a deficit is persistent or systemic, then it must be that the combination of the time preference and the set of other factors makes it so. A financial model can be developed to accept the combination of factors in order to project the current and future deficits. The estimates of those factors become assumptions. A discount rate, which is like an interest rate, can be used to represent the time preference. The process will make the intertemporal choice. The opposite sides of a political argument might both be critical of the assumptions but each side might find bias in a different estimate.
Wikipedia says of the Treaty of Maastricht...
One of the obligations of the treaty for the members was to keep
"sound fiscal policies, with debt limited to 60% of GDP and annual
deficits no greater than 3% of GDP".
There can be punishment for breaking the rules...
the EU Member States added, with the Treaty of Maastricht, a new
provision to the EC Treaty which seeks to secure respect for ECJ
judgments. The new procedure according to Article 228 of the EC
Treaty is a special judicial procedure for the enforcement of
judgments that provides for the imposition of penalty payments or lump
sums by the ECJ on a Member State which fails to comply with an
earlier judgment of the ECJ that a Member State is in breach of its
obligations under Community law
If there is persistence in rule breaking it might mean that there is a preference for risking the punishment.
The general observations about behaviour can be applied to a specific case. Since Reuters reports that "France's budget deficit is likely to overshoot the European Union's limit of 3 percent of GDP next year and stand at around 3.2 percent" it means that there is a preference in France for risking the punishment.
Notice that the punishment is for enforcing the ECJ judgment so first a country would have to fight in court, lose and face a judgment, ignore the judgment. Since there is a process to be followed there is not any immediate risk of punishment.